|
| Status |
Public on Dec 06, 2017 |
| Title |
RNAseq_piwi_mut_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
piwi_mut
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: F1 piwi homozygous progeny: (females) [Harwich]; piwi[2]/CyO; [Harwich] vs. (males) w[1118]; piwi[1]/CyO, w+
developmental stage: Adult
tissue: Ovary
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Flies were grown at standard conditions at 29º C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Poly(A)-selected RNA-sequencing (RNA-seq) was performed on 2.5µg of RNA purified from adult ovaries using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®.
Total RNA from adult ovaries was isolated using Trizol reagent (Invitrogen) and quantified by Qubit (Invitrogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Poly(A)-selected RNA-seq from piwi mutant (in Harwich background)
|
| Data processing |
ChIP-seq analysis was performed on the Galaxy web-based platform following previously described methods (Han et al, 2015 - Bioinformatics). Illumina adaptors and other low quality sequences were removed using the ‘Trim Galore!’ package. ChIP-seq input and IP filtered data were mapped to the Drosophila genome (dm3) and transposon consensus sequences using Bowtie2, using the -k = 1 parameter.
RNA-seq: Paired-end (100-nt-long reads) RNA-seq data were mapped to the Drosophila melanogaster genome (dm3) and the FlyBase and Repbase transposon consensus database using the piPipes package (version 1.5.0; https://github.com/bowhan/piPipes), following the RNA-seq pipeline as previously described (Han et al., 2015 - Bioinformatics). Briefly, libraries were first aligned to ribosomal RNA using Bowtie2. Non-rRNA reads were then mapped to the transcriptome and transposon consensus using Bowtie2.
Genome_build: Drosophila melanogaster dm3
Supplementary_files_format_and_content: ChIP-seq: Files contain density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: RNA-seq: Files contain strand-specific density coverage of uniquely mapped reads to dm3
|
| |
|
| Submission date |
Sep 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Felipe Karam Teixeira |
| E-mail(s) |
Felipe.Teixeira@med.nyu.edu
|
| Organization name |
New York University Medical Center
|
| Department |
Skirball Institute
|
| Street address |
540 1st Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE103582 |
piRNA-mediated regulation of transposon alternative splicing in soma and germline |
|
| Relations |
| Reanalyzed by |
GSM3284032 |
| BioSample |
SAMN07613301 |
| SRA |
SRX3166329 |
