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Sample GSM1833191 Query DataSets for GSM1833191
Status Public on Oct 15, 2015
Title CG9754_het_rep2_smRNAseq
Sample type SRA
 
Source name adult fly ovaries
Organism Drosophila melanogaster
Characteristics tissue: ovaries
Treatment protocol Flies were fed with yeast paste. Germline specific knockdowns were done as described (Czech et al., 2013 Mol Cell).
Growth protocol Flies were raised at 25°C on standard cornmeal-molasses agar medium.
Extracted molecule total RNA
Extraction protocol Total RNA from ovaries of 2-3 day old females of the indicated knockdowns was isolated using TRIzol (Invitrogen).
Small libraries were prepared as described (Czech et al., 2013 Mol Cell).
small RNA cloning (End cloning)
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina MiSeq
 
Description small RNA sequencing
Data processing Demultiplexed, concatenated files with the 50nt or 76nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome (dm3) using nexalign. Only reads that met these conditions were subjected to further analyses.
For annotations we used a combination of UCSC [dm3], miRBase [release 14], and Flybase [r5.26] tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request). For comparison of small RNA counts between samples, libraries of dsRNA-white samples were set to one million reads. Next, all libraries were normalized based on unique mappers to the flamenco (for nos-GAL4 knockdowns) piRNA clusters.
Genome_build: dm3/2006
Supplementary_files_format_and_content: Excel file contains read counts of small RNAs (24 nt to 29 nt) mapping to antisense transposon consensus normalized to total miRNA reads comparing CG9754 heterozygous and mutant in sheet "het_vs_mut_CG9754". In sheet "untethered_vs_tethered", read counts of small RNAs (24 nt to 29 nt) mapping to piRNA clusters are shown.
 
Submission date Jul 27, 2015
Last update date May 15, 2019
Contact name Yang Yu
E-mail(s) yyu@cshl.edu
Organization name Cold Spring Harbor Laboratory
Lab Hannon Lab
Street address One Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL16479
Series (2)
GSE71372 Panoramix enforces piRNA-dependent co-transcriptional silencing (small RNA-Seq)
GSE71374 Panoramix enforces piRNA-dependent co-transcriptional silencing
Relations
BioSample SAMN03939115
SRA SRX1120745

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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