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Sample GSM1914750 Query DataSets for GSM1914750
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
 
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 SAMN04201800
SRA SRX1361350

Supplementary file Size Download File type/resource
GSM1914750_HP1_291C_siGFP.bedgraph.gz 89.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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