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Sample GSM1124784 Query DataSets for GSM1124784
Status Public on Apr 29, 2013
Title H1d-2
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: Embryonic stem cells
strain: C57BL/6-129/Sv
passages: 10-20
epitope tagged protein: FLAG-H1d Knock-in
chip antibody: FLAG (Sigma, F3165)
Growth protocol ESCs were cultured on mitotically inactivated mouse embryonic fibroblasts feeder layers in ESC media consisted of DMEM supplemented with 15% FBS, non-essential amino acids, β-mercaptoethanol, nucleotides and LIF.
Extracted molecule genomic DNA
Extraction protocol Soluble chromatin lysates were extracted from sonicated nuclei and protein-DNA complexes were immunoprecipitated with antibody.
The libraries were prepared from 10 ng of immunoprecipiated DNA or input DNA using Illumina ChIP-seq Sample Preparation Kit and purified with a Qiagen DNA Isolation column.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Sequencing was performed with Illumina Genome Analyzer II and Illumina HiSeq 2000 systems. Raw sequence reads containing more than 30% of 'N' were removed and adaptor sequences were trimmed.
Clean sequences were aligned against mouse genome mm9 using Bowtie aligner software
IP-IN signals were calculated by subtraction of tag counts/100bp window/10 million mappable reads of ChIP-seq library (IP) by that of its corresponding input-seq library (IN) using GenPlay software.
aligned.bed files were generated from bowtie alignment. IP-IN.bed and IP-IN.wig files were obtained from Genplay software.
Genome_build: mm9
Supplementary_files_format_and_content: IP-IN.wig files
Submission date Apr 17, 2013
Last update date May 15, 2019
Contact name Yuhong Fan
Organization name Georgia Institute of Technology
Department School of Biology and the Petit Institute for Bioengineering and Bioscience
Street address IBB 2313, 315 Ferst Drive
City Atlanta
State/province Georgia
ZIP/Postal code 30332
Country USA
Platform ID GPL13112
Series (1)
GSE46134 High Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells
BioSample SAMN02046888
SRA SRX266820

Supplementary file Size Download File type/resource
GSM1124784_H1d-2_IP-IN.wig.gz 214.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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