|
| Status |
Public on Apr 13, 2012 |
| Title |
Ovaries_3d_RL(low capacity to repress) |
| Sample type |
SRA |
| |
|
| Source name |
3-day-old ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Cha-RL
gender: female
tissue: ovaries
age: 3 days
|
| Treatment protocol |
Small RNAs (18-30nt) were isolated using anion-exchange chromatography extractions.
|
| Growth protocol |
Flies were grown at 23 degrees C on standard Drosophila food.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted small RNAs between 18 and 30 nucleotides were selected on an acrylamide gel and cloned.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Small RNAs from reactive females (Cha-R) with young maternal ancestors
|
| Data processing |
RL3d.bonafide_counts.txt; genome build: dm5
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed.
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode, miRNAs from miRBase, transcripts from Flybase and transposable elements from Repbase and from the UCSC repeatmasker track.
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNA, the remainder, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.
|
| |
|
| Submission date |
Dec 16, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
SEVERINE CHAMBEYRON |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Department |
Institute of Human Genetics
|
| Lab |
Non-coding RNA, epigenetics and genome stability
|
| Street address |
141, rue de la Cardonille
|
| City |
MONTPELLIER |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE34506 |
piRNA-mediated transgenerational inheritance of an acquired trait |
|
| Relations |
| SRA |
SRX112022 |
| BioSample |
SAMN00766299 |
