|
Status |
Public on Nov 19, 2015 |
Title |
mRNA-seq from SetDB1-KD siRNA #3 |
Sample type |
SRA |
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|
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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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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 |