|
| Status |
Public on Nov 19, 2015 |
| Title |
anti-Rpb3 ChIP-seq in Su(var)3-9-KD used in Fig6 |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian Somatic Cells (OSC)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
chip-seq antibody: anti-Rpb3 (Adelman et al. Mol Cell 2005)
genotype/variation: Su(var)3-9-KD
|
| 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 |
genomic DNA |
| 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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)
reads were trimmed to bases 6-45 using HomerTools, version 3.9; N-containing reads were discarded; smaller than 40nt-long reads were discarded
reads were mapped with bowtie v0.12.7 (-v 1 -k 1 -m 1 --best --strata) to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1
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 |
| BioSample |
SAMN04201810 |
| SRA |
SRX1361360 |
