Difference between revisions of "FlyBase:Clone Report"
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The '''Clone Report''' provides information on clones. The report includes information on the type of clone, the sequence of the clone insert (if available), the library that a clone is associated with, and the vector into which the insert is spliced. | The '''Clone Report''' provides information on clones. The report includes information on the type of clone, the sequence of the clone insert (if available), the library that a clone is associated with, and the vector into which the insert is spliced. | ||
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This field is only filled in for clones that are linked to a library that was produced from a known fly strain. | This field is only filled in for clones that are linked to a library that was produced from a known fly strain. | ||
|- | |- | ||
| − | |''' | + | |'''Vector''' || The name of the vector into which the insert was cloned. |
| + | If the vector has been curated by FlyBase this field will link to a Transgenic Construct report for this vector. | ||
| + | |} | ||
| + | {| class="wikitable" style="width: 100%;" | ||
| + | |- | ||
| + | |'''Tissue Source'''||colspan='2'|The tissue that provided the starting material to generate the clone. | ||
This field is only filled in for clones that are linked to a library that was produced from a known tissue source. | This field is only filled in for clones that are linked to a library that was produced from a known tissue source. | ||
|- | |- | ||
| − | |||
| − | + | |'''Stage''' || style="width: 33%;"| '''Tissue/Position''' || style="width: 33%;"|'''Reference''' | |
| + | |- | ||
| + | | Term from FlyBase Development controlled vocabulary, e.g. third instar larval stage || Term from FlyBase Anatomy controlled vocabulary, e.g. eye disc ||| Publication(s) that describe(s) the library. | ||
| + | |||
|} | |} | ||
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|'''Total bases''' || style="width: 80%;" | Is the length in bases of the insert sequence. | |'''Total bases''' || style="width: 80%;" | Is the length in bases of the insert sequence. | ||
|- | |- | ||
| − | |''' | + | |'''NCBI''' || Is the NCBI accession number for the sequence record. This field provides a link to the NCBI record of this sequence. |
|- | |- | ||
|'''Sequence data''' || Is the actual sequence residues associated with insert sequence. | |'''Sequence data''' || Is the actual sequence residues associated with insert sequence. | ||
|} | |} | ||
| − | == | + | ==Library Information== |
| − | Free text | + | {| class="wikitable" style="width: 100%;" |
| + | |- | ||
| + | |'''Description''' || style="width: 80%;" | A simple description of the library/reagent collection. | ||
| + | |- | ||
| + | |'''Sample preparation''' || Free text description of key experimental details in the growth, treatment and isolation of the source biological material. | ||
| + | |- | ||
| + | |'''Protocol''' || Free text description of key molecular experimental details in the construction of the library. | ||
| + | |- | ||
| + | |'''Comment''' || Free text describing additional aspects of the library. | ||
| + | |- | ||
| + | |'''Reported As/Symbol Synonyms''' || A list of symbols that have been used in the literature, or by FlyBase, to describe the library. | ||
| + | |- | ||
| + | |'''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. | ||
| + | |} | ||
==External Crossreferences and Linkouts== | ==External Crossreferences and Linkouts== | ||
Latest revision as of 21:00, 13 December 2017
Last Updated: 12 December 2017
The Clone Report provides information on clones. The report includes information on the type of clone, the sequence of the clone insert (if available), the library that a clone is associated with, and the vector into which the insert is spliced.
FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication if they wish. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data.
General Information
| Symbol | The valid symbol that is used in FlyBase for the clone.
The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the symbol is used throughout FlyBase. For D.melanogaster clones, the species prefix is only displayed in the GENERAL INFORMATION section at the top of a Report. |
| Name | The valid name that is used in FlyBase for the clone. |
| Feature type | A single controlled vocabulary term from the Sequence Ontology (SO), which aims to describe the key type of the clone. Currently there are reports available for clones of type 'cDNA_clone' and 'genomic_clone'. |
| Species | The organism that the clone insert originates from, with the initial letter of the genus and the full species name listed. |
| FlyBase ID | The Primary FlyBase identifier number of the clone, used to uniquely identify the clone in the database.
A clone may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Clone Report. |
| Computed gene | This field only contains information for cDNA clones.
It specifies the symbol of the gene that the clone is calculated to derive from, and provides a link to the relevant gene report. |
| Collection Status | Indicates if a clone has been designated as part of a recognized collection (e.g. the DGC gold collection) |
| Known Problems | Known problems: If a clone insert has been identified as problematic in some way then a controlled statement to this effect is reported in this field. For clones contributed by the BDGP, problems they identified. Examples: chimeric clone, genomic DNA, incomplete CDS, contains transposon sequences, No poly A tail, unspliced intron, reverse transcriptase error. |
| FlyBase Assessment | FlyBase assessment: Problems identified by FlyBase. Examples: chimeric clone, genomic DNA, contains transposon sequences, aberrant intron, reverse transcriptase error, polymerase error, contains extraneous sequence, caution: significant strain polymorphism(s), suspect. (Note that FlyBase does not flag incomplete clones.) FlyBase also flags modified clones and the cDNAs they are derived from: "This corrected cDNA clone replaces ..." and "Caution: This cDNA clone replaced by ..." |
| Library | The name of the library to which a clone belongs. Additional information about the library can be found in later fields of the Clone Report. In some cases a clone has not been associated with a library and in those cases this field will be empty.
Clicking on the symbol takes you to the associated Large Dataset Metadata Report |
| Strain | The strain from which this clone was generated.
This field is only filled in for clones that are linked to a library that was produced from a known fly strain. |
| Vector | The name of the vector into which the insert was cloned.
If the vector has been curated by FlyBase this field will link to a Transgenic Construct report for this vector. |
| Tissue Source | The tissue that provided the starting material to generate the clone.
This field is only filled in for clones that are linked to a library that was produced from a known tissue source. | |
| Stage | Tissue/Position | Reference |
| Term from FlyBase Development controlled vocabulary, e.g. third instar larval stage | Term from FlyBase Anatomy controlled vocabulary, e.g. eye disc | Publication(s) that describe(s) the library. |
Sequence Data of the Insert
If a clone insert has been completely sequenced then information about this sequence is given in the Full length sequence section. If only a partial sequence has been determined for a clone insert then information about 5', 3' or both sequences are presented.
| Total bases | Is the length in bases of the insert sequence. |
| NCBI | Is the NCBI accession number for the sequence record. This field provides a link to the NCBI record of this sequence. |
| Sequence data | Is the actual sequence residues associated with insert sequence. |
Library Information
| Description | A simple description of the library/reagent collection. |
| Sample preparation | Free text description of key experimental details in the growth, treatment and isolation of the source biological material. |
| Protocol | Free text description of key molecular experimental details in the construction of the library. |
| Comment | Free text describing additional aspects of the library. |
| Reported As/Symbol Synonyms | A list of symbols that have been used in the literature, or by FlyBase, to describe the library. |
| 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. |
External Crossreferences and Linkouts
A complete list of links to external databases for the Clone. The Linkouts section contains Linkouts. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived.
Synonyms & Secondary IDs
Reported As
| Symbol synonym | A list of symbols that have been used in the literature, or by FlyBase, to describe the clone. |
Secondary FlyBase IDs
A list of Secondary FlyBase identifier numbers of the clone.
If a clone 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. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.
References
A list of publications that discuss the clone, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Clone Report.