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Status |
Public on Nov 19, 2015 |
Title |
anti-HP1 ChIP-seq with 291C Ab in GFP-KD |
Sample type |
SRA |
|
|
Source name |
Ovarian Somatic Cells (OSC)
|
Organism |
Drosophila melanogaster |
Characteristics |
chip-seq antibody: anti-HP1, Covance (#291C) genotype/variation: 291C Ab in GFP-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
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|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
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) 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
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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 |
BioSample |
SAMN04201800 |
SRA |
SRX1361350 |