|
| 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 |
