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Sample GSM1212799 Query DataSets for GSM1212799
Status Public on Sep 12, 2013
Title EED+/+ ESC Pou5f1 replicate 2 read counts
Sample type SRA
Source name cell culture
Organism Mus musculus
Characteristics cell type: EED+/+ ESCs
strain: 17Rn5-3354SB
genotype: EED+/+
Growth protocol standard cell culture
Extracted molecule genomic DNA
Extraction protocol submitter has not supplied any information
submitter has not supplied any information
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description sibling wild-type to Eed mutant ESC line
Data processing Two to seven 4C libraries were multiplexed and sequenced using the Illumina Genome Analyzer II to obtain 76 base pair (bp) reads or Illumina HIseq-2000 to obtain 100 bp reads.
The resultant reads were mapped to the mouse genome using Bowtie software (Langmead et al., 2009). Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis.
Reads that were successfully aligned to the genome were then remapped to the 736,199 unique HindIII sites along the genome (with respect to the 50bp upstream and downstream of the site) by matching their respective loci.
Genome_build: MM9
Supplementary_files_format_and_content: bedGraph-formatted files contain unqiue HindIII loci and associated 4C-seq read counts
Submission date Aug 20, 2013
Last update date May 15, 2019
Contact name Kathrin Plath
Organization name UCLA
Street address 615 Charles E. Young Drive South
City Los Angeles
ZIP/Postal code 90095
Country USA
Platform ID GPL13112
Series (1)
GSE50029 Long-range chromatin contacts reveal a role for the pluripotency and Polycomb networks in genome organization
BioSample SAMN02319447
SRA SRX337225

Supplementary file Size Download File type/resource
GSM1212799_EedWT_ESC_Pou5f1_2_readcounts.bedGraph.gz 4.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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