|
Status |
Public on Dec 06, 2017 |
Title |
RNAseq_piwi_het_rep1 |
Sample type |
SRA |
|
|
Source name |
piwi_het
|
Organism |
Drosophila melanogaster |
Characteristics |
genotype: F1 piwi heterozygous 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)
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|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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|
Description |
Poly(A)-selected RNA-seq from piwi heterozygous (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
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|
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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 |
GSM3284030 |
BioSample |
SAMN07613304 |
SRA |
SRX3166326 |