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Sample GSM1914740 Query DataSets for GSM1914740
Status Public on Nov 19, 2015
Title mRNA-seq from SetDB1-KD siRNA #3
Sample type SRA
 
Source name Ovarian Somatic Cells (OSC)
Organism Drosophila melanogaster
Characteristics genotype/variation: SetDB1-KD siRNA
Treatment protocol OSC were transfected twice with siRNAs and analyzed after 4 days
Growth protocol OSC were cultured as described in Niki et al 2007
Extracted molecule total RNA
Extraction protocol for RNA-seq and small RNA-seq the total RNA was extracted using TRIZOL Reagent (Invitrogen)
for ChIP chromatin was prepared and extracted as in Lee et all 2006
small-RNAs were cloned as described in Senti et al 2015
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files containing 2nd mate were reverse complemented and used together with fastq files containing 1st mate as single-end library; N-containing reads were discarded
reads were trimmed to high-quality bases 6-46 using HomerTools, version 4.1 and after filtering (masking reads aliging to Drosophila and human rRNA, C virus, mitochondrial sequences ), mapped to genome dm3 with bowtie v0.12.7 (-m 1 -k 1 --best --strata -v 1) using in-house developed pipeline
RPKM was calculated using HomerTools (analyzeRepeats.pl rna -count exons -condenseGenes -rpkm -strand +); for differential gene expression counts were calculated with HomerTools (analyzeRepeats.pl rna dm3 -count exons -condenseGenes -noadj -strand +) follwed by (getDiffExpression.pl -repeats -DESeq)
Supplementary_files_format_and_content: RNA-seq: file contains strand-specific density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ChIP-seq: file contains density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ncRNA-seq: file contains collapsed, dm3 genome-aligned reads
Genome_build: dmel_release 5
 
Submission date Oct 20, 2015
Last update date May 15, 2019
Contact name Grzegorz Sienski
E-mail(s) grzegorz.sienski@imba.oeaw.ac.at
Organization name IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences
Street address Dr. Bohr-Gasse 3
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL13304
Series (1)
GSE74097 Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery
Relations
Reanalyzed by GSM3277362
BioSample SAMN04201790
SRA SRX1361340

Supplementary file Size Download File type/resource
GSM1914740_egg_3-KD_minus_uni_reads.bw 45.1 Mb (ftp)(http) BW
GSM1914740_egg_3-KD_plus_uni_reads.bw 43.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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