|
| Status |
Public on Apr 08, 2015 |
| Title |
IP-tj-GAL4>Ø |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovary
genotype: tj-Gal4/+
antibody: anti-FLAG antibody (Sigma A2220) ; anti-HA antibody (Santa-Cruz SC805)
|
| Growth protocol |
Flies were grown at 20 degrees °C exept in the last 5 days (25°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Aliquot of precleared ovary lysates were saved as input.
A double FLAG-HA (anti-FLAG antibody (Sigma A2220); anti-HA antibody (Santa-Cruz SC805)) a immunoprecipitation was parformed on precleared lysates and RNAs from both inputs and IPs were Trizol extracted and rRNA depleted.
RNAs were fragmented (zinc treatment Illumina protocol), reverse transcribed by random hexamer primers, 260 to 280 bp fragments (ie, insert of 160-240nt) were purified from acrylamide gels by Fasteris SA (Switzerland).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Drosha-IP RNA
RNA Trizol extraction
|
| Data processing |
Sequenced reads were stripped of the adapter in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) according to sequencing quality using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed (one mismatch was nevertheless allowed on low-sequencing quality nucleotides).
Mapped reads were further mapped on a data base made from miRNA retrieved from miRBase (http://www.mirbase.org/)
Genome_build: Drosophila melanogaster (release 5)
Supplementary_files_format_and_content: Simple tabulated format where column 1 represents genome localisation, column 2 the miRNA name and column 3 the corresponding read counts
|
| |
|
| Submission date |
Sep 02, 2014 |
| 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 (2) |
| GSE60973 |
MicroRNA-dependent transposable element transcriptional silencing in Drosophila somatic ovarian cells [RIP-Seq] |
| GSE60974 |
MicroRNA-dependent transposable element transcriptional silencing in Drosophila somatic ovarian cells |
|
| Relations |
| BioSample |
SAMN03014956 |
| SRA |
SRX690640 |
