Difference between revisions of "FlyBase:ModENCODE data at FlyBase"

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Revision as of 17:51, 4 March 2023

WARNING

This page is under construction. The link to this temp page is below. https://wiki.flybase.org/wiki/FlyBase:FlyBase_Help_Index#Tools_and_Downloads_Documentation Once this page is finalized, it's intended to replace content at this page. https://wiki.flybase.org/wiki/FlyBase:ModENCODE_RNA-Seq_Overview Once the replacement is complete, delete this page and links to it.

Overview

FlyBase offers a subset of modENCODE datasets that characterize gene expression and transcriptional regulation in Drosophila. The modENCODE datasets incorporated by FlyBase often represent high-level distillations of data, combining or synthesizing data from multiple modENCODE experiments, rather than the raw data from individual experiments. Most modENCODE datasets at FlyBase are available through JBrowse; in some cases, modENCODE data has been combined with data from other non-modENCODE datasets. For RNA-seq datasets, FlyBase provides additional query/analysis tools, as well download files and data displays on gene reports. FlyBase dataset reports provide descriptions of how data was generated and analyzed, as well as links to the original raw data at data repositories.

Please note: While FlyBase hosts a selection of tools for browsing and using modENCODE data, it is not an exhaustive resource for all data generated from the modENCODE project.

RNA-Seq Query Tools and Browsers

The primary RNA-Seq data in FlyBase are the modENCODE data originally published in Graveley et al., 2011 and Brown et al., 2014, comprising 30 developmental stage expression profiles, 29 tissue expression profiles, 25 treatment/condition expression profiles and 24 cell line expression profiles. RNA-Seq reads were mapped to the Release 6 genome assembly as described in Brown et al., 2014; note that data for replicates of a given biological condition were combined. In JBrowse genomic views, several other RNA-Seq datasets are also presented, but the RNA-Seq query tools are restricted to the modENCODE datasets.

A series of video tutorials describing different RNA-Seq tools is available. See

RNA-Seq Data In JBrowse

FlyBase JBrowse has several tracks that display RNA-Seq expression profiles, which give coverage values base-by-base across the genome. Choose datasets for expression by stage, tissue, treatments, or cell lines. By default, the many tracks are displayed in the layered FlyBase “TopoView” format, and data are shown on a log2 scale, since they range over many orders of magnitude. Customization options are offered to help drill down into the data, accessed by clicking on the down arrow in the track title bar.

Alternate RNA-Seq Views
  • Space the data out. Increase the “vertical spacing between samples to prevent strong signal from one sample from obscuring the profile behind it.
  • Align the profiles. Change the “Samples presentation style” from “Tilted” (default) to “Vertical” to remove the horizontal offset between adjacent RNA-Seq profiles so that they align horizontally to the same genome position.
  • Choose the appropriate scaling method. Log2 scaling provides the best dynamic range for viewing both low and high signal together. Linear scaling is preferable in regions with high baseline signal, and provides a more intuitive view of the relative change in signal.

Additional JBrowse tracks display discrete transcription start sites, exon junctions and RNA A-to-I editing sites identified by analysis of modENCODE RNA-Seq data. The exon junction and editing site tracks also include additional data from non-modENCODE experiments.

RNA-Seq JBrowse Track Listing

JBrowse tracks sourced from modENCODE data (in part or in full) can be enabled via the “Available Tracks” menu on the left pane of the JBrowse viewer. These tracks include:

Track section Track name FlyBase Dataset(s) JBrowse Track Description
Transcript Level Features
>Transcription Start Sites (TSS) 		TSS (modENCODE, embryo) mE_Transcription_Start_Sites Transcription Start Site Tracks
Transcript Level Features RNA-Seq exon junctions modENCODE_mRNA-Seq_U_junctions RNA-Seq Exon Junction Tracks
Transcript Level Features RNA Editing Sites mE_A-to-I_RNA_Editing_Sites RNA Editing Site Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes 		Developmental stages modENCODE_mRNA-Seq_development RNA-Seq Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes 		Cell lines modENCODE_mRNA-Seq_cell.B RNA-Seq Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes 		Treatments/Conditions modENCODE_mRNA-Seq_treatments RNA-Seq Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes
  >Tissues 		Digestive system mE_mRNA_L3_Wand_dig_sys
mE_mRNA_A_1d_dig_sys
mE_mRNA_A_4d_dig_sys
mE_mRNA_A_20d_dig_sys 		RNA-Seq Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes
  >Tissues 		Fat body and salivary glands mE_mRNA_L3_Wand_fat
mE_mRNA_WPP_fat
mE_mRNA_P8_fat
mE_mRNA_L3_Wand_saliv
mE_mRNA_WPP_saliv 		RNA-Seq Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes
  >Tissues 		Imaginal disc and other carcass mE_mRNA_L3_Wand_imag_disc
mE_mRNA_L3_Wand_carcass
mE_mRNA_A_1d_carcass
mE_mRNA_A_4d_carcass
mE_mRNA_A_20d_carcass 		RNA-Seq Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes
  >Tissues 		CNS and adult head mE_mRNA_L3_CNS
mE_mRNA_P8_CNS
mE_mRNA_A_MateM_1d_head
mE_mRNA_A_MateM_4d_head
mE_mRNA_A_MateM_20d_head
mE_mRNA_A_VirF_1d_head
mE_mRNA_A_VirF_4d_head
mE_mRNA_A_VirF_20d_head
mE_mRNA_A_MateF_1d_head
mE_mRNA_A_MateF_4d_head
mE_mRNA_A_MateF_20d_head 		RNA-Seq Tracks
Expression
>RNA-Seq
 >modENCODE Transcriptomes
  >Tissues 		Gonads and male accessory glands mE_mRNA_A_MateM_4d_testis
mE_mRNA_A_MateM_4d_acc_gland
mE_mRNA_A_VirF_4d_ovary
mE_mRNA_A_MateF_4d_ovary 		RNA-Seq Tracks

The FlyBase JBrowse wig files are available for download on the FlyBase FTP site. Note that FlyBase wig files are slightly different from the standard wig format, in that the optional "span" parameter is implied (not explicitly declared): for example, for a run of 5 nucleotides on chr 2L having the same value at each position, only the value for the first position is declared, without the preceding "variableStep chrom=chr2L span=5" information.

RNA-Seq RPKM Data

For most modENCODE RNA-Seq samples, FlyBase calculated the "RPKM" gene expression level within the exonic extent of the gene, as described in Gelbart and Emmert, 2013. These RPKM values are recalculated with each FlyBase release to account for changes in gene transcript structure. For the purposes of presentation and queries, values were assigned to one of eight bins, from very low to extremely high. These RPKM values are displayed on gene reports (see the "Expression Data > High-Throughput Expression Data" section) and can be downloaded from directly from the gene report. RPKM data for all genes can be downloaded from the "Genes" section of the Downloads page.

RNA-Seq Profile

Go to RNA-Seq Part II: Using RNA-Seq Profile Search to see the associated video tutorial.

RNA-Seq Profile is a fine grained query tool, powered by modENCODE high-throughput RNA-Seq expression data (using FlyBase-computed RPKM expression values), that allows you to find genes with specific patterns of expression across several variables. Interested in development of the central nervous system? Search for genes that are expressed in these tissues during a specific developmental stage. Curious how toxins affect the fly reproductive system? Search for genes expressed in fly gonads that are activated (or suppressed) by exposure to Paraquat or Rotenone.

Choose datasets for expression by stage, tissue, treatments, or cell lines, or use several datasets in conjunction. Each dataset is presented in a form that allows you to select either narrow slices of the data, or larger sections for more coverage. You also have control over the levels of expression used in the search, allowing you to define distinct thresholds for the ON and OFF states. Keep in mind that extremely narrow search conditions may produce sparse or empty result sets. Feel free to experiment; the tool will remember your settings so that you can adjust, instead of needing to re-enter them. Search results can be exported, as usual, for further analysis or download.

NB: The group check box selectors are interpreted differently depending on whether you are making selections from the 'Expression ON' or 'Expression OFF' sections. 'Expression ON' selectors: Selecting multiple stages using one of the grouping check boxes acts as an 'OR'. This means that if a gene is expressed at or above the chosen expression level in any one or more of the selected stages it will be returned in the result list. To get 'AND' behavior (i.e., return only those genes which are expressed at the chosen level in each one of the selected stages) you must select each of the stages individually. 'Expression OFF' selectors: Selecting multiple stages using one of the grouping check boxes acts as an 'AND'. This means that for a gene to be returned in the result list, the observed level of expression must be at or below the selected level in all of the selected group stages. Therefore, for the 'expression OFF' selectors, checking a group check box is functionally identical to selecting each individual sub-category.

RNA-Seq Similarity

Go to RNA Seq Part III: Searching for Similarly Expressed Genes to see the associated video tutorial.

RNA-Seq Similarity finds genes with expression patterns that are similar to that of a given gene; this search option can also be launched from the relevant gene page. 'Similar to' in this case means that the pattern of higher and lower expression1 in the categories for the RNA-Seq expression experiment data you choose are close to those of your chosen gene, as measured by the correlation coefficient2 between the data for your given gene and each of the search result genes. Enter your query gene symbol in the box, and choose to search for genes with similar expression by developmental stage, tissue, treatments, or cell lines. You can also specify a subset of experimental samples within a set of RNA-Seq expression data to use when making comparisons. The resulting genes can be exported to a FlyBase hit list.

1 Note that two expression patterns will be flagged as similar if the profile of peaks and troughs of expression have a similar shape, even though one expression pattern may have much higher or lower values overall.

2 FlyBase uses a generalized Spearman rank correlation for this statistic.

RNA-Seq By Region

RNA-Seq By Region can be used to compare the RNA-Seq signal for a given region across samples, or to compare signal between two regions within a single sample.

Supply the symbol or FBgn ID for one gene of interest, and choose to query either the developmental or tissue RNA-Seq profiles. The tool will retrieve the locations of all exons for the gene specified, and report an average RNA-Seq signal for each region. Values are normalized for read depth across a given set, and reported as values from 1 to 50; very high read values are truncated at a value of 50. Alternatively, input one or more genomic regions using standard GBrowse coordinate nomenclature (e.g., X:350000..351000) and the tool will return the average RNA-Seq signal for each submitted genomic span; for multiple regions, enter one region per line in the input box.

For fast visual inspection of the potentially large expression tables, the background of table cells is colored in the same way as in the heatmap coloring schema of expression histograms in FlyBase gene reports. These tables can be copied and downloaded and used for further analysis.

Note that the signal reported for a given region may arise from the expression of multiple transcripts from one or more genes; the tool simply reports the total signal for that region and does not attempt to assign the expression in that region to any specific transcript.

Download RNA-Seq Data

Each FlyBase analysis tool described above offers a way to download the results.

RPKM data for a specific gene can be downloaded from directly from the gene report "Expression Data" section. RPKM data for all genes can be downloaded from the "Genes" section of the Downloads page.

FlyBase JBrowse wig files are available for download on the FlyBase FTP site. Note that the format is more compact: for a run of nucleotides having the same coverage value, only the first nucleotide in the run is declared in the file.

Transcriptional Regulation Datasets

Transcriptional Regulation Data In JBrowse

FlyBase JBrowse has several tracks that display regions of distinct chromatin configurations, origins of replication, insulators, and transcription factor binding sites (TFBS), determined by ChIP-chip and ChIP-Seq experiments.

Transcriptional Regulation JBrowse Track Listing

JBrowse tracks describing aspects of chromatin and transcriptional regulation that were sourced from modENCODE data can be enabled via the “Available Tracks” menu on the left pane of the JBrowse viewer. These tracks are all located in the Genome Level Features track section and are listed in the table below.

Track section Track name FlyBase Dataset(s) JBrowse Track Description
Genome Level Features
>Chromatin Features 		Chromatin Domains (9-state model, S2 cells) Chromatin_types_mE1.S2 Chromatin Feature Tracks
Genome Level Features
>Chromatin Features 		Chromatin Domains (9-state model, BG3 cells) Chromatin_types_mE1.BG3 Chromatin Feature Tracks
Genome Level Features
>Transcriptional Regulatory Elements 		Insulators (modENCODE, class I) Insulator_Class_I.mE01 Transcriptional Regulatory Elements Tracks
Genome Level Features
>Transcriptional Regulatory Elements 		Insulators (modENCODE, class II) Insulator_Class_II.mE01 Transcriptional Regulatory Elements Tracks
Genome Level Features
>Transcriptional Regulatory Elements 		Putative PREs (modENCODE) mE1_HDAC_PRE Transcriptional Regulatory Elements Tracks
Genome Level Features
>Transcription Factor Binding Sites (TFBS)
 >TFBS (modENCODE, ChIP-chip, whole embryo) 		whole embryo, TFBS HOT spot analysis mE1_TFBS_HSA TFBS Tracks
Genome Level Features
>Transcription Factor Binding Sites (TFBS)
 >TFBS (modENCODE, ChIP-chip, whole embryo) 		whole embryo, ZINC Finger TFBS mE1_TFBS_disco
mE1_TFBS_ftz-f1
mE1_TFBS_GATAe
BDTNP1_TFBS_hb
mE1_TFBS_hkb
BDTNP1_TFBS_kni
mE1_TFBS_Kr
mE1_TFBS_sbb
mE1_TFBS_sens
BDTNP1_TFBS_shn
BDTNP1_TFBS_sna
BDTNP1_TFBS_tll
mE1_TFBS_zfh1
 TFBS Tracks
Genome Level Features
>Transcription Factor Binding Sites (TFBS)
 >TFBS (modENCODE, ChIP-chip, whole embryo) 		whole embryo, Homeodomain TFBS BDTNP1_TFBS_bcd
mE1_TFBS_cad
mE1_TFBS_Dll
mE1_TFBS_en
mE1_TFBS_eve
BDTNP1_TFBS_ftz
mE1_TFBS_inv
BDTNP1_TFBS_prd
mE1_TFBS_Ubx
BDTNP1_TFBS_z
TFBS Tracks
Genome Level Features
>Transcription Factor Binding Sites (TFBS)
 >TFBS (modENCODE, ChIP-chip, whole embryo) 		whole embryo, Helix-loop-helix TFBS BDTNP1_TFBS_da
mE1_TFBS_h
mE1_TFBS_kn
BDTNP1_TFBS_twi
TFBS Tracks
Genome Level Features
>Transcription Factor Binding Sites (TFBS)
 >TFBS (modENCODE, ChIP-chip, whole embryo) 		whole embryo, BTB/POS ChIP TFBS mE1_TFBS_bab1
mE1_TFBS_chinmo
mE1_TFBS_Trl
mE1_TFBS_ttk
TFBS Tracks
Genome Level Features
>Transcription Factor Binding Sites (TFBS)
 >TFBS (modENCODE, ChIP-chip, whole embryo) 		whole embryo, Other classes TFBS mE1_TFBS_cnc
mE1_TFBS_D
BDTNP1_TFBS_dl
BDTNP1_TFBS_gt
mE1_TFBS_jumu
BDTNP1_TFBS_Mad
BDTNP1_TFBS_Med
mE1_TFBS_run
BDTNP1_TFBS_slp1
mE1_TFBS_Stat92E
TFBS Tracks
Genome Level Features
>Other Sequence Elements 		Origins of replication (modENCODE, Kc, S2, BG3 cells) mE_Early_Replication_Origins_cells Other Sequence Element Tracks

Download Data

For JBrowse tracks representing discrete regions (like ChIP binding regions, chromatin domains, etc), the locations of those features can be downloaded using the JBrowse track menu (at the top left of the track), for either the region in view or the entire chromosome scaffold being viewed, in GFF3, BED or Sequin formats. Unfortunately, download of genome-wide data for a given JBrowse track is not supported.
Currently, the only way to download genome-wide data for a given dataset in JBrowse is to parse it from the single large FlyBase GFF file that powers FlyBase JBrowse, using dataset name and/or FlyBase "FBlc" identifier in column 9 of the GFF file: e.g., _Library=mE1_TFBS_chinmo:FBlc0000289.

Finding Your modENCODE Dataset of Interest

Below is a list of all FlyBase datasets representing modENCODE data, along with modENCODE, NCBI GEO and SRA identifiers. FlyBase datasets offer succinct descriptions of the sample prep and data analysis methods. For raw data, please follow links to NCBI GEO or SRA. If you can't find your modENCODE dataset of interest, we recommend searching for the dataset at NCBI GEO or dataMED. If searching using the modENCODE identifier, it may be helpful to add modencode_ or modencode_submission_ as a prefix to the identifier.

data_type flybase_dataset species dataset_type dataset_title modencode_submission_ids ncbi_bioproject_ids ncbi_geo_ids sra_ids flybase_representation
Expression [https:flybase.org/reports/FBlc0000260.html modENCODE_mRNA-Seq_cell.B] D. melanogaster project Transcriptional profile of D. melanogaster cell lines, stranded RNA-Seq, modENCODE. 555 PRJNA75285 SRP003893 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001414.html RNA-Seq_mE4391_1182-4H] D. melanogaster assay RNA-Seq of D. melanogaster, 1182-4H cell line, modENCODE. 4391 SRX029185 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001415.html RNA-Seq_mE4392_CME-L1] D. melanogaster assay RNA-Seq of D. melanogaster, CME-L1 cell line, modENCODE. 4392 SRX029186
SRX029187 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001312.html RNA-Seq_mE5955_CME-W1-Cl.8+] D. melanogaster assay RNA-Seq of D. melanogaster, CME-W1-Cl.8+ cell line, modENCODE, unstranded. 5955 GSM390061
GSM390062 		SRX003834
SRX003835 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001408.html RNA-Seq_mE4393_CME-W2] D. melanogaster assay RNA-Seq of D. melanogaster, CME-W2 cell line, modENCODE. 4393 SRX029188
SRX029189
SRX045355 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001431.html RNA-Seq_mE5966_fGS-OSS] D. melanogaster assay RNA-Seq of D. melanogaster, fGS/OSS cell line, modENCODE. 5966 SRX149409 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001409.html RNA-Seq_mE4394_GM2] D. melanogaster assay RNA-Seq of D. melanogaster, GM2 cell line, modENCODE. 4394 SRX029190
SRX029191
SRX029192 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001315.html RNA-Seq_mE4395_Kc167] D. melanogaster assay RNA-Seq of D. melanogaster, Kc167 cell line, modENCODE, unstranded. 5952 GSM390059
GSM390060 		SRX003836
SRX003837 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001410.html RNA-Seq_mE4396_mbn2] D. melanogaster assay RNA-Seq of D. melanogaster, mbn2 cell line, modENCODE. 4396 SRX029196
SRX045354 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001417.html RNA-Seq_mE4397_ML-DmBG1-c1] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmBG1-c1 cell line, modENCODE. 4397 SRX029199 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001411.html RNA-Seq_mE4398_ML-DmBG2-c2] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmBG2-c2 cell line, modENCODE. 4398 SRX029197
SRX029198
SRX045357 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001313.html RNA-Seq_mE5954_ML-DmBG3-c2] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmBG3-c2 cell line, modENCODE, unstranded. 5954 GSM390065
GSM390066 		SRX003838
SRX003839 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001418.html RNA-Seq_mE4399_ML-DmD11] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD11 cell line, modENCODE. 4399 SRX029200
SRX029201
SRX045356 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001419.html RNA-Seq_mE4400_ML-DmD16-c3] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD16-c3 cell line, modENCODE. 4400 SRX029202
SRX029203 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001420.html RNA-Seq_mE4401_ML-DmD17-c3] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD17-c3 cell line, modENCODE. 4401 SRX029204
SRX029205 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001412.html RNA-Seq_mE4402_ML-DmD20-c5] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD20-c5 cell line, modENCODE. 4402 SRX029206
SRX045353 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001421.html RNA-Seq_mE4403_ML-DmD21] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD21 cell line, modENCODE. 4403 SRX029207 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001422.html RNA-Seq_mE4404_ML-DmD32] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD32 cell line, modENCODE. 4404 SRX029208
SRX029209
SRX045358 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001423.html RNA-Seq_mE4405_ML-DmD4-c1] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD4-c1 cell line, modENCODE. 4405 SRX029210
SRX045359 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001424.html RNA-Seq_mE4406_ML-DmD8] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD8 cell line, modENCODE. 4406 SRX029211 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001425.html RNA-Seq_mE4407_ML-DmD9] D. melanogaster assay RNA-Seq of D. melanogaster, ML-DmD9 cell line, modENCODE. 4407 SRX029212 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001430.html RNA-Seq_mE5965_OSC] D. melanogaster assay RNA-Seq of D. melanogaster, OSC cell line, modENCODE. 5965 SRX149408 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001429.html RNA-Seq_mE5964_OSS] D. melanogaster assay RNA-Seq of D. melanogaster, OSS cell line, modENCODE. 5964 SRX149407 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001426.html RNA-Seq_mE4408_S1] D. melanogaster assay RNA-Seq of D. melanogaster, S1 cell line, modENCODE. 4408 SRX029213
SRX029214
SRX045352 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001314.html RNA-Seq_mE5953_S2-DRSC] D. melanogaster assay RNA-Seq of D. melanogaster, S2-DRSC cell line, modENCODE, unstranded. 5953 GSM390063
GSM390064 		SRX003840
SRX003841 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001427.html RNA-Seq_mE4409_S2R+] D. melanogaster assay RNA-Seq of D. melanogaster, S2R+ cell line, modENCODE. 4409 SRX029215
SRX029216
SRX029217
SRX246395
SRX246396
SRX246397
SRX246398
SRX246399
SRX246400 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001413.html RNA-Seq_mE4410_S3] D. melanogaster assay RNA-Seq of D. melanogaster, S3 cell line, modENCODE. 4410 SRX029218
SRX045351 		Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001428.html RNA-Seq_mE4411_Sg4] D. melanogaster assay RNA-Seq of D. melanogaster, Sg4 cell line, modENCODE. 4411 SRX029219 Cell Lines: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0000085.html modENCODE_mRNA-Seq_development] D. melanogaster project Transcriptional profile of D. melanogaster developmental stages, unstranded RNA-Seq, modENCODE. 574 PRJNA75285 SRP001065 Developmental stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001341.html RNA-Seq_mE4433_AF_1d] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, adult female (1 day post-eclosion), modENCODE, unstranded. 4433 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001343.html RNA-Seq_mE4434_AF_30d] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, adult female (30 days post-eclosion), modENCODE, unstranded. 4434 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001342.html RNA-Seq_mE4435_AF_5d] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, adult female (5 days post-eclosion), modENCODE, unstranded. 4435 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001344.html RNA-Seq_mE4436_AM_1d] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, adult male (1 day post-eclosion), modENCODE, unstranded. 4436 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001346.html RNA-Seq_mE4437_AM_30d] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, adult male (30 days post-eclosion), modENCODE, unstranded. 4437 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001345.html RNA-Seq_mE4438_AM_5d] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, adult male (5 days post-eclosion), modENCODE, unstranded. 4438 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001317.html RNA-Seq_mE4439_E1-4] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (0-2hr AEL), modENCODE, unstranded. 4439 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001322.html RNA-Seq_mE4440_E13-15] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (10-12hr AEL), modENCODE, unstranded. 4440 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001323.html RNA-Seq_mE4441_E15-16] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (12-14hr AEL), modENCODE, unstranded. 4441 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001324.html RNA-Seq_mE4442_E16] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (14-16hr AEL), modENCODE, unstranded. 4442 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001325.html RNA-Seq_mE4443_E17(i)] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (16-18hr AEL), modENCODE, unstranded. 4443 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001326.html RNA-Seq_mE4444_E17(ii)] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (18-20hr AEL), modENCODE, unstranded. 4444 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001318.html RNA-Seq_mE4447_E4-9] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (2-4hr AEL), modENCODE, unstranded. 4447 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001327.html RNA-Seq_mE4445_E17(iii)] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (20-22hr AEL), modENCODE, unstranded. 4445 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001328.html RNA-Seq_mE4446_E17(iv)] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (22-24hr AEL), modENCODE, unstranded. 4446 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001319.html RNA-Seq_mE4448_E9-11] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (4-6hr AEL), modENCODE, unstranded. 4448 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001320.html RNA-Seq_mE4449_E11-12] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (6-8hr AEL), modENCODE, unstranded. 4449 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001321.html RNA-Seq_mE4450_E12-13] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo (8-10hr AEL), modENCODE, unstranded. 4450 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001329.html RNA-Seq_mE4451_L1] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, larva (L1), modENCODE, unstranded. 4451 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001330.html RNA-Seq_mE4452_L2] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, larva (L2), modENCODE, unstranded. 4452 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001331.html RNA-Seq_mE4453_L3_12hr] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, larva (L3, 12hr post-molt), modENCODE, unstranded. 4453 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001334.html RNA-Seq_mE4456_L3_PS7-9] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, larva (L3, clear gut), modENCODE, unstranded. 4456 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001332.html RNA-Seq_mE4454_L3_PS1-2] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, larva (L3, dark gut), modENCODE, unstranded. 4454 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001333.html RNA-Seq_mE4455_L3_PS3-6] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, larva (L3, light gut), modENCODE, unstranded. 4455 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001338.html RNA-Seq_mE4459_P8] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, pharate adult (2 days APF), modENCODE, unstranded. 4459 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001339.html RNA-Seq_mE4460_P9-10] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, pharate adult (3 days APF), modENCODE, unstranded. 4460 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001340.html RNA-Seq_mE4461_P15] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, pharate adult (4 days APF), modENCODE, unstranded. 4461 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001336.html RNA-Seq_mE4457_P5] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, pupa (12hr APF), modENCODE, unstranded. 4457 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001337.html RNA-Seq_mE4458_P6] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, pupa (24hr APF), modENCODE, unstranded. 4458 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001335.html RNA-Seq_mE4462_WPP] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, white prepupa, modENCODE, unstranded. 4462 SRX007811
SRX008180
SRX008227
SRX008238
SRX008258 		Developmental Stages: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0000206.html modENCODE_mRNA-Seq_tissues] D. melanogaster project Transcriptional profile of D. melanogaster tissues, stranded RNA-Seq, modENCODE. 3207 PRJNA75285 SRP003905 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001369.html RNA-Seq_mE4250_A_1d_carcass] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (1 day), carcass. 4250 SRX029379
SRX029380 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001370.html RNA-Seq_mE4251_A_1d_digestive_system] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (1 day), digestive system. 4251 SRX029381
SRX029382 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001371.html RNA-Seq_mE4252_A_20d_carcass] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (20 days), carcass. 4252 SRX029383
SRX029384 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001372.html RNA-Seq_mE4253_A_20d_digestive_system] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (20 days), digestive system. 4253 SRX029385
SRX029386
SRX045360 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001397.html RNA-Seq_mE4276_A_4d_Cd_0.05M] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 0.05M cadmium treatment. 4276 SRX043503
SRX047234 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001396.html RNA-Seq_mE4279_A_4d_Cd_0.1M] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 0.1M cadmium treatment. 4279 SRX043506 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001401.html RNA-Seq_mE4285_A_4d_Paraquat_10mM] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 10mM paraquat treatment. 4285 SRX043509 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001391.html RNA-Seq_mE4283_A_4d_Cu_15mM] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 15mM copper treatment. 4283 SRX043508 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001394.html RNA-Seq_mE4274_A_4d_Caffeine_2.5mg/ml] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 2.5mg/ml caffeine treatment. 4274 SRX043501 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001393.html RNA-Seq_mE4275_A_4d_Caffeine_25mg/ml] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 25mg/ml caffeine treatment. 4275 SRX043502 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001392.html RNA-Seq_mE4289_A_4d_Zn_4.5mM] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 4.5mM zinc treatment. 4289 SRX043513 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001400.html RNA-Seq_mE4286_A_4d_Paraquat_5mM] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), 5mM paraquat treatment. 4286 SRX043510
SRX047233 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001387.html RNA-Seq_mE4280_A_4d_Cold1] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), cold treatment 1. 4280 SRX043515 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001388.html RNA-Seq_mE4281_A_4d_Cold2] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), cold treatment 2. 4281 SRX043516 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001407.html RNA-Seq_mE4284_A_4d_Heatshock] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 day), heat shock treatment. 4284 SRX043517 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001373.html RNA-Seq_mE4254_A_4d_carcass] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 days), carcass. 4254 SRX029387
SRX029388 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001374.html RNA-Seq_mE4255_A_4d_digestive_system] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult (4 days), digestive system. 4255 SRX029389
SRX029390
SRX045361 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001358.html RNA-Seq_mE4241_AF_mated_1d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (1 day), mated, head. 4241 SRX029367
SRX042017 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001361.html RNA-Seq_mE4263_AF_virgin_1d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (1 day), virgin, head. 4263 SRX029391
SRX042024 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001363.html RNA-Seq_mE4242_AF_mated_20d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (20 days), mated, head. 4242 SRX029368
SRX042018
SRX045504
SRX048965 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001382.html RNA-Seq_mE4264_AF_virgin_20d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (20 days), virgin, head. 4264 SRX029392
SRX029393
SRX042025 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001364.html RNA-Seq_mE4243_AF_mated_4d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (4 days), mated, head. 4243 SRX029369 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001359.html RNA-Seq_mE4244_AF_mated_4d_ovary] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (4 days), mated, ovary. 4244 SRX029370
SRX042019
SRX042020 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001362.html RNA-Seq_mE4265_AF_virgin_4d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (4 days), virgin, head. 4265 SRX029394
SRX042026
SRX042027 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001383.html RNA-Seq_mE4266_AF_virgin_4d_ovary] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult female (4 days), virgin, ovary. 4266 SRX029395
SRX029396 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001360.html RNA-Seq_mE4245_AM_mated_1d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult male (1 day), mated, head. 4245 SRX029371
SRX042021 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001365.html RNA-Seq_mE4246_AM_mated_20d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult male (20 days), mated, head. 4246 SRX029372
SRX029373 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001366.html RNA-Seq_mE4247_AM_mated_4d_accessory_gland] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult male (4 days), mated, accessory gland. 4247 SRX029374
SRX029375
SRX042022
SRX048961
SRX099848 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001367.html RNA-Seq_mE4248_AM_mated_4d_head] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult male (4 days), mated, head. 4248 SRX029376
SRX029377 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001368.html RNA-Seq_mE4249_AM_mated_4d_testis] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, adult male (4 days), mated, testis. 4249 SRX029378
SRX042023
SRX099849 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001375.html RNA-Seq_mE4256_P8_CNS] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, pharate adult (stage P8), CNS. 4256 SRX029404
SRX042030 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001386.html RNA-Seq_mE4267_P8_fat_body] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, pharate adult (stage P8), fat body. 4267 SRX029405
SRX029406 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0000236.html modENCODE_mRNA-Seq_treatments] D. melanogaster project Transcriptional profile of D. melanogaster response to various treatments, stranded RNA-Seq, modENCODE. 3724 PRJNA75165 SRP005712 Treatments/Conditions: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001389.html RNA-Seq_mE4282_L3_Cu_0.5mM] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 0.5mM copper treatment. 4282 SRX043507 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001395.html RNA-Seq_mE4273_L3_Caffeine_1.5mg/ml] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 1.5mg/ml caffeine treatment. 4273 SRX043500 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001404.html RNA-Seq_mE4270_L3_EtOH_10] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 10% ethanol treatment. 4270 SRX043497 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001398.html RNA-Seq_mE4277_L3_Cd_12h] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 12hr 0.05M cadmium treatment. 4277 SRX043504 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001406.html RNA-Seq_mE4271_L3_EtOH_2.5] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 2.5% ethanol treatment. 4271 SRX043498 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001403.html RNA-Seq_mE4287_L3_Rotenone_2ug] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 2ug/ml rotenone treatment. 4287 SRX043511 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001405.html RNA-Seq_mE4272_L3_EtOH_5] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 5% ethanol treatment. 4272 SRX043499 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001390.html RNA-Seq_mE4290_L3_late_Zn_5mM] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 5mM zinc treatment. 4290 SRX043514 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001399.html RNA-Seq_mE4278_L3_Cd_6hr] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 6hr 0.05M cadmium treatment. 4278 SRX043505 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001402.html RNA-Seq_mE4288_L3_Rotenone_8ug] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, 8ug/ml rotenone treatment. 4288 SRX043512 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001377.html RNA-Seq_mE4258_L3_carcass] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, carcass. 4258 SRX029397
SRX042028 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001376.html RNA-Seq_mE4257_L3_CNS] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, CNS. 4257 SRX029398 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001378.html RNA-Seq_mE4259_L3_digestive_system] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, digestive system. 4259 SRX029399
SRX042029 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001379.html RNA-Seq_mE4260_L3_fat_body] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, fat body. 4260 SRX029400 Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001380.html RNA-Seq_mE4261_L3_imaginal_disc] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, imaginal disc. 4261 SRX029401
SRX045362
SRX099850 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001381.html RNA-Seq_mE4262_L3_salivary_gland] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, third instar larva, salivary gland. 4262 SRX029402
SRX029403 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001384.html RNA-Seq_mE4268_WPP_fat_body] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, white prepupa, fat body. 4268 SRX029407
SRX029408 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001385.html RNA-Seq_mE4269_WPP_salivary_gland] D. melanogaster assay RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, white prepupa, salivary gland. 4269 SRX029409
SRX042031 		Tissues: RPKM, JBrowse coverage, analysis tools (profile, region, similarity)
Expression [https:flybase.org/reports/FBlc0001098.html RNA-Seq_mE3085_Dpse_AM_head] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, MV2-25 strain, adult male head. 3085 GSM499404 FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0001099.html RNA-Seq_mE3086_Dpse_AF_head] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, MV2-25 strain, adult female head. 3086 GSM499403 FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0001100.html RNA-Seq_mE3620_Dpse_AM] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, adult male. 3620 GSM694281
GSM694282 		FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0001101.html RNA-Seq_mE3621_Dpse_AF] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, adult female. 3621 GSM694279
GSM694280 		FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0001117.html RNA-Seq_mE4049_Dpse_AF_ovary] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, adult female ovary. 4049 GSM775498
GSM775499 		FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0001118.html RNA-Seq_mE4047_Dpse_AF_carcass] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, adult female carcass. 4047 GSM775494
GSM775495 		FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0001119.html RNA-Seq_mE4050_Dpse_AM_testis] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, adult male testis. 4050 GSM775500
GSM775501 		FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0001120.html RNA-Seq_mE4048_Dpse_AM_carcass] D. pseudoobscura pseudoobscura assay RNA-Seq of D. pseudoobscura, adult male carcass. 4048 GSM775496
GSM775497 		FlyBase JBrowse wig file available for download.
Expression [https:flybase.org/reports/FBlc0000040.html RM_cDNA] D. melanogaster assay cDNA sequences of D. melanogaster, iso-1 strain, embryo, 5' ends of capped transcripts. 34 JBrowse: TSS (modENCODE, embryo)
Expression [https:flybase.org/reports/FBlc0000049.html RP_cDNA] D. melanogaster assay RNA-Seq of D. melanogaster, iso-1 strain, embryo, 5' ends of capped transcripts. 1041|1042|1043|1044 JBrowse: TSS (modENCODE, embryo)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0000200.html Chromatin_types_mE2.BG3] D. melanogaster result 9-state chromatin model derived from analysis of histone modification ChIP, ML-DmBG3-c2 cells. 3362 JBrowse: Chromatin Domains (9-state model, BG3 cells)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0000199.html Chromatin_types_mE1.S2] D. melanogaster result 9-state chromatin model derived from analysis of histone modification ChIP, S2-DRSC cells. 3363 JBrowse: Chromatin Domains (9-state model, S2 cells)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0000058.html Insulator_Class_I.mE01] D. melanogaster result Insulators (type I) identified by ChIP-chip of Cp190, BEAF-32 and CTCF in embryos. 2946 JBrowse: Insulators (modENCODE, class I)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0000059.html Insulator_Class_II.mE01] D. melanogaster result Insulators (type II) identified by ChIP-chip of su(Hw) in embryos. 2946 JBrowse: Insulators (modENCODE, class II)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0000188.html mE_Early_Replication_Origins_cells] D. melanogaster result Early replication origins, analysis of three cell lines (meta-peaks). 3441 JBrowse: Origins of replication (modENCODE, Kc, S2, BG3 cells)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003160.html ChIP-chip_mE2559_HDAC1_E1-15] D. melanogaster assay ChIP-chip of HDAC1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 2559 GSE25956 JBrowse: Putative PREs (modENCODE)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003161.html ChIP-chip_mE2560_HDAC1_E1-15] D. melanogaster assay ChIP-chip of HDAC1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 2560 GSE25957 JBrowse: Putative PREs (modENCODE)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003166.html ChIP-chip_mE2563_HDAC4_E1-15] D. melanogaster assay ChIP-chip of HDAC4 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 2563 GSE25960 JBrowse: Putative PREs (modENCODE)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003167.html ChIP-chip_mE2564_HDAC4_E1-15] D. melanogaster assay ChIP-chip of HDAC4 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 2564 GSE25961 JBrowse: Putative PREs (modENCODE)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003189.html ChIP-chip_mE919_H3K27me3_E1-15] D. melanogaster assay ChIP-chip of H3K27me3 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 919 GSE16245 JBrowse: Putative PREs (modENCODE)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003190.html ChIP-chip_mE622_H3K4me3_E1-15] D. melanogaster assay ChIP-chip of H3K4me3 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 622 GSE15980
GSE16245 		JBrowse: Putative PREs (modENCODE)
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003210.html ChIP-chip_mE2574_hairy_E1-12] D. melanogaster assay ChIP-chip of hairy in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL). 2574 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
whole embyro, Helix-loop-helix TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003213.html ChIP-chip_mE618_kn_E1-15] D. melanogaster assay ChIP-chip of kn in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 618 GSE15984 JBrowse: whole embryo, TFBS HOT spot analysis
whole embyro, Helix-loop-helix TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003219.html ChIP-chip_mE615_ttk_E1-15] D. melanogaster assay ChIP-chip of ttk in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 615 GSE15987 JBrowse: whole embryo, TFBS HOT spot analysis
whole embryo, BTB/POS ChIP TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003225.html ChIP-chip_mE628_bab1_E1-15] D. melanogaster assay ChIP-chip of bab1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 628 GSE15908 JBrowse: whole embryo, TFBS HOT spot analysis
whole embryo, BTB/POS ChIP TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003228.html ChIP-chip_mE23_Trl_E1-15] D. melanogaster assay ChIP-chip of Trl in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 23 GSE16245 JBrowse: whole embryo, TFBS HOT spot analysis
whole embryo, BTB/POS ChIP TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003232.html ChIP-chip_mE608_chinmo_E1-15] D. melanogaster assay ChIP-chip of chinmo in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 608 GSE15959 JBrowse: whole embryo, TFBS HOT spot analysis
whole embryo, BTB/POS ChIP TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003198.html ChIP-chip_mE606_Dll_E1-15] D. melanogaster assay ChIP-chip of Dll in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 606 GSE15963 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003199.html ChIP-chip_mE2578_cad_E9-12] D. melanogaster assay ChIP-chip of cad in D. melanogaster, cad-GFP, embryo (4-8 hr AEL). 2578 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003200.html ChIP-chip_mE902_cad_E1-9] D. melanogaster assay ChIP-chip of cad in D. melanogaster, cad-GFP, embryo (0-4 hr AEL). 902 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003201.html ChIP-Seq_mE2626_cad_E1-9] D. melanogaster assay ChIP-Seq of cad in D. melanogaster, cad-GFP, embryo (0-4 hr AEL). 2626 GSE20000 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003202.html ChIP-chip_mE2570_cad_E1-9] D. melanogaster assay ChIP-chip of cad in D. melanogaster, iso-1 strain, embryo (0-4 hr AEL). 2570 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003203.html ChIP-Seq_mE2637_cad_E9-12] D. melanogaster assay ChIP-Seq of cad in D. melanogaster, cad-GFP, embryo (4-8 hr AEL). 2637 GSE20000 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003207.html ChIP-chip_mE625_en_E1-15] D. melanogaster assay ChIP-chip of en in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 625 GSE15964 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003208.html ChIP-chip_mE2603_eve_E3-11] D. melanogaster assay ChIP-chip of eve in D. melanogaster, eve-YFP, embryo (1-6 hr AEL). 2603 GSE26221 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003211.html ChIP-chip_mE605_inv_E1-15] D. melanogaster assay ChIP-chip of inv in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 605 GSE15982 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003212.html ChIP-chip_mE619_inv_E1-15] D. melanogaster assay ChIP-chip of inv in D. melanogaster, inv-GFP, embryo (0-12 hr AEL). 619 GSE15983 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003220.html ChIP-chip_mE614_Ubx_E1-15] D. melanogaster assay ChIP-chip of Ubx in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 614 GSE15988 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003221.html ChIP-chip_mE613_Ubx_E7-12] D. melanogaster assay ChIP-chip of Ubx in D. melanogaster, iso-1 strain, embryo (3-8 hr AEL). 613 GSE15992 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003222.html ChIP-chip_mE612_Ubx_E7-12] D. melanogaster assay ChIP-chip of Ubx in D. melanogaster, iso-1 strain, embryo (3-8 hr AEL). 612 GSE15993 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003223.html ChIP-chip_mE603_Ubx_E7-12] D. melanogaster assay ChIP-chip of Ubx in D. melanogaster, iso-1 strain, embryo (3-8 hr AEL). 603 GSE15994 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, homeodomain TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003204.html ChIP-chip_mE626_Dichaete_E1-15] D. melanogaster assay ChIP-chip of Dichaete in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 626 GSE15927 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, Other classes TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003205.html ChIP-chip_mE2571_Dichaete_E1-12] D. melanogaster assay ChIP-chip of Dichaete in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL). 2571 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, Other classes TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003218.html ChIP-chip_mE617_run_E1-15] D. melanogaster assay ChIP-chip of run in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 617 GSE15985 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, Other classes TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003229.html ChIP-chip_mE2576_jumu_E1-12] D. melanogaster assay ChIP-chip of jumu in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL). 2576 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, Other classes TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003230.html ChIP-chip_mE616_Stat92E_E1-15] D. melanogaster assay ChIP-chip of Stat92E in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 616 GSE15986 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, Other classes TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003234.html ChIP-chip_mE627_cnc_E1-15] D. melanogaster assay ChIP-chip of cnc in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 627 GSE15926 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, Other classes TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003206.html ChIP-chip_mE2572_disco_E1-12] D. melanogaster assay ChIP-chip of disco in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL). 2572 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003209.html ChIP-chip_mE624_ftz-f1_E1-15] D. melanogaster assay ChIP-chip of ftz-f1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 624 GSE15965 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003214.html ChIP-chip_mE898_Kr_E1-12] D. melanogaster assay ChIP-chip of Kr in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL). 898 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003215.html ChIP-chip_mE979_sens_E9-12] D. melanogaster assay ChIP-chip of sens in D. melanogaster, sens-GFP, embryo (4-8 hr AEL). 979 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003216.html ChIP-chip_mE978_sens_E9-12] D. melanogaster assay ChIP-chip of sens in D. melanogaster, iso-1 strain, embryo (4-8 hr AEL). 978 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003217.html ChIP-chip_mE2577_sens_E9-12] D. melanogaster assay ChIP-chip of sens in D. melanogaster, iso-1 strain, embryo (4-8 hr AEL). 2577 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003224.html ChIP-chip_mE604_zfh1_E1-15] D. melanogaster assay ChIP-chip of zfh1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 604 GSE15989 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003226.html ChIP-chip_mE609_sbb_E1-15] D. melanogaster assay ChIP-chip of sbb in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL). 609 GSE15958 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003227.html ChIP-chip_mE2569_sbb_E1-9] D. melanogaster assay ChIP-chip of sbb in D. melanogaster, iso-1 strain, embryo (0-4 hr AEL). 2569 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003231.html ChIP-chip_mE2573_GATAe_E1-12] D. melanogaster assay ChIP-chip of GATAe in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL). 2573 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
Chromatin/Transcriptional Regulation [https:flybase.org/reports/FBlc0003233.html ChIP-chip_mE2575_hkb_E1-12] D. melanogaster assay ChIP-chip of hkb in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL). 2575 GSE25259 JBrowse: whole embryo, TFBS HOT spot analysis
JBrowse: whole embryo, ZINC Finger TFBS
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