|
| Status |
Public on Apr 27, 2017 |
| Title |
white-embKD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: vasa-GAL80[ts]/+;;da-GAL4/shwhite
embryonic temperature: 28°C
|
| Growth protocol |
Flies were maintained at 18°C. After appropriate cross, embryos were shifted at 28°C to induce either RNAi against white or piwi proteins.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from ovaries using TRIzol. 4µg of total RNA were subjected to Ribo-Zero ribosomal depletion (Epicenter). RNA was further purified using RNA Clean & Concentrator-5 (Zymo Research).
Library construction and 150nt paired-end read sequencing were performed by Donnelly Sequencing Centre (Toronto) on an Illumina NextSeq 500. The RNA-seq experiments were done in two biological replicates.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribo-Zero (Epicenter) ribosomal depletion total RNA further purified using RNA Clean & Concentrator-5 (Zymo Research)
|
| Data processing |
Read mapping on D. melanogaster genome and canonical transposons: For each sample, paired-end raw data was analyzed using the piPipes RNA-Seq pipeline (doi:10.1093/bioinformatics/btu647) with default options. Raw data files ending in *R1_001.fastq.gz correspond to the left reads (option "-l") and those ending in *R2_001.fastq.gz correspond to right reads (option "-r"). Release 5 of D. melanogaster genome was used (option "-g dm3"). Reads are first mapped to rRNA sequences using bowtie2. Reads that do not map at this first step are mapped to the genome using STAR. The mapping results are then processed by cufflinks in order to determine a normalization factor based on reads mapping on genes. The reads are then mapped on the gene and transposon sequences using bowtie2, and the mapping results are processed with express for quantification. Quantification by express is then normalized using the cufflinks-determined gene-mapping read abundance. All these steps were performed by piPipes (commit number cd5f1cfb33e67ddf2926cea7ad57212b17695e27, october 14th 2015).
Genome_build: Drosophila melanogaster, release 5
Supplementary_files_format_and_content: The processed data consist in two tab-separated columns. The first column contains gene and transposon identifiers, and the second column contains the corresponding normalized quantification, as obtained by piPipes.
|
| |
|
| Submission date |
Jun 10, 2016 |
| 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 |
GPL19132 |
| Series (2) |
| GSE83235 |
Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries [RNA-seq] |
| GSE83238 |
Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries |
|
| Relations |
| Reanalyzed by |
GSM3281369 |
| BioSample |
SAMN05226689 |
| SRA |
SRX1837302 |
