Difference between revisions of "FlyBase:Large Dataset Metadata Report"
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|'''Assay platform''' || Any microarrays or sequencing platforms used in the assay. | |'''Assay platform''' || Any microarrays or sequencing platforms used in the assay. | ||
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| − | |'''Data analysis''' || Free text descriptions of key experimental details in the processing of raw data. | + | |'''Data analysis''' || Free text descriptions of key experimental details in the processing of raw data. This includes mapping of next generation sequencing reads to the genome, normalization of genome-wide data, and peak calling methods. |
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Revision as of 20:47, 24 June 2015
Last Updated: 24 June 2015
The Large Dataset Metadata Report provides information on large datasets and reagent collections and associated metadata. The report includes information on the type of dataset or collection, the biological source of material (species, strain, cell line, tissue, developmental stage), reagents used (vectors, assay platforms), and experimental details. The report also lists FlyBase features that are associated with the dataset (e.g, stocks, constructs, sequence features). Links to data repositories and reagent sources are provided when possible.
General Information
| Name | The name that FlyBase uses for this dataset. |
| Species | The organism from which biological material for the dataset was derived. |
| Collection Type | The type of dataset or collection. |
| FlyBase ID | The FlyBase identifier number of the dataset, used to uniquely identify the dataset in the database. |
Source & Content
| Consists of | A simple description of the type of data or reagents represented by the dataset/collection. |
| Created by | The lab or resource that generated the dataset or reagent collection described. Links are provided when possible. |
| Available from | A resource where the reagents described can be obtained (for reagent collections only). |
| Strain | The fly strain used as the source of biological material. |
Stage & Tissue
| Stage | Tissue/Position | Reference |
|---|---|---|
| The developmental stage used as the source of biological material. | The tissue used as the source of biological material. | The reference from which the sample information was obtained. |
| Cell Line | The cell line used as the source of biological material. |
Recent Updates
This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms).
Description & Members
| Description | A concise description of the dataset. |
| Parent collections | Related datasets are organized into hierarchies. The parent collections listed in this section may represent an umbrella report that represents a group of similar datasets, or a high level dataset that synthesizes multiple underlying datasets. |
| Component collections | The component collections listed in this section represent similar datasets grouped under the reported dataset, or alternatively component datasets used to generate a given high level synthesized dataset. |
| Number in collection | The number of objects grouped under the dataset (e.g., cDNAs, stocks, RNA-Seq reads or binding sites). |
| Comment on number in collection | The type of objects grouped under the dataset. |
| Members | Click on the "Download list of members" button to get a list of the objects grouped by the dataset. |
Experimental Protocol
| Vector | Any vectors used in the generation of the dataset or reagent collection. |
| Sample preparation | Free text descriptions of key experimental details in the growth, treatment and isolation of the source biological material. |
| Collection preparation | Free text descriptions of key experimental details in the further processing of biological material. |
| Mode of assay | The assay used in the dataset. |
| Assay platform | Any microarrays or sequencing platforms used in the assay. |
| Data analysis | Free text descriptions of key experimental details in the processing of raw data. This includes mapping of next generation sequencing reads to the genome, normalization of genome-wide data, and peak calling methods. |
Additional data
| More information is available under: | Comments on additional information available from other websites, data repositories or files on the FlyBase FTP server. |
| Accessions | Links to dataset accessions at public data repositories like NCBI GEO or SRA. |
| Associated files | Links to associated data files on FlyBase FTP server. |
| Additional sites | Links to sites with more information about the data. |
Synonyms & Secondary IDs
Reported As
| Symbol Synonym | A list of symbols that have been used in the literature, or by FlyBase, to describe the dataset. |
Secondary FlyBase IDs
A list of Secondary FlyBase identifier numbers of the dataset. If a dataset has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database.
References
The number in parentheses indicates the number of references listed. A list of publications that discuss the dataset, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual dataset report.