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| Status |
Public on Jan 01, 2014 |
| Title |
Iso1a-Solexa-5' |
| Sample type |
SRA |
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| Source name |
ovary cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
line: iso1a
cage: yes
normalization: no
strandedness: yes
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For samples 1 & 2, total RNA were extracted from 20 ovaries following provider procedure for the RNAqueous kit (Ambion) and 5 µgr were treated by GATC to obtain PolyA+ RNA devoided of tRNA and rRNA. For samples 3 to 5, we extracted polyA+ each from full bodies from 10 adult males (<24 hour) and 10 adult females (0-3 days), and sequenced using Illumina HiSeq technology after random primed retrotranscription.
Libraries were constructed using standard454 and Illumina instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Sample 2
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| Data processing |
Adapters were first removed using S-MART tools.
Sample 2 was mapped with Blat, the other samples were mapped with Bowtie. In all samples, only unique, without errors, hits were kept.
We counted the number of hits per gene and transposable elements using the S-MART tools.
FlyBase (release 06/29/11) has been used for the gene annotation. Transposable elements were annotated by the REPET pipe-line (see article).
Genome_build: dmel5
Supplementary_files_format_and_content: For each sample, a 2-column .tab flat file gives the number of hit per transcript, and a GFF3 file gives the number hit per transposable element copy.
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| Submission date |
Nov 18, 2013 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Matthias Zytnicki |
| Organization name |
INRA
|
| Department |
Applied Mathematics and Informatics
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| Lab |
MIAT
|
| Street address |
24, Chemin de Borde-Rouge
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| City |
Castanet |
| ZIP/Postal code |
31326 |
| Country |
France |
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| Platform ID |
GPL11203 |
| Series (1) |
| GSE52472 |
Non-canonical TSSs of TEs alter gene structure and expression in Drosophila melanogaster |
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| Relations |
| BioSample |
SAMN02404831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1267494_sample2Genes.tab.gz |
33.2 Kb |
(ftp)(http) |
TAB |
| GSM1267494_sample2Tes.gff3.gz |
845.2 Kb |
(ftp)(http) |
GFF3 |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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