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Sample GSM1174404 Query DataSets for GSM1174404
Status Public on Aug 01, 2013
Title PolII ChIP-seq from Control-KD
Sample type SRA
 
Source name EGFP-KD_PolII ChIP-seq
Organism Drosophila melanogaster
Characteristics cell type: Ovarian Somatic Cells (OSC)
transfected with: siRNA against EGFP
chip antibody: anti-Pol II antibody 8WG16
chip antibody vendor: Santa Cruz
chip antibody cat. #: sc-56767
chip antibody lot #: A1712
Treatment protocol OSC were transfected once with siRNAs and analyzed after 2 days
Growth protocol Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium)
Extracted molecule genomic DNA
Extraction protocol Crosslinking chomatin was sheared to 200bp using a Covaris S2 ultrasonicators, immunoprecipitated using anti-Pol II antibody 8WG16 (Santa Cruz). After reversing the cross-linking, samples were treated with RNase A and then DNA was recovered. 
The deep sequencing libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (NEB)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description Sample 7
Data processing Sequenced reads were trimmed for adaptor sequence using cutadapt software, then mapped to dm3 whole genome and repbase transposable elements using bowtie2 v2.0.0 with default parameters
For calculation of Reads Per Million mapped reads (RPM) of transposable elements, dm3 genome and repbase transposable element mapping result was processed using in-house perl script. In short, number of reads falling in the transposable elements were counted and normalized by the count of genome mapped reads.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include tag density for each transposable element (normalized by Reads Per Million mapped reads (RPM))
 
Submission date Jun 26, 2013
Last update date Jul 03, 2021
Contact name Yuka W. Iwasaki
E-mail(s) iwasaki@keio.jp
Organization name Keio University School of Medicine
Department Department of Molecular Biology
Lab Siomi Lab
Street address 35 Shinanomachi, Shinjuku-ku,
City Tokyo
ZIP/Postal code 160-8582
Country Japan
 
Platform ID GPL16479
Series (1)
GSE47006 Expression profile and RNA Polymerase II occupancy of transposable elements among knock down of the piRNA pathway components in OSCs
Relations
BioSample SAMN02213900
SRA SRX315132

Supplementary file Size Download File type/resource
GSM1174404_PolIIChIP_siEGFPtags.txt.gz 1.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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