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Sample GSM1856450 Query DataSets for GSM1856450
Status Public on Dec 07, 2015
Title ChIPseq_Suz12_2i_BR2
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics developmental stage: E14
chip antibody: Suz12 (Anti-Suz12, ab1207, Abcam)
Treatment protocol 2i mESCs were grown in serum free NDiff 227 supplemented with MEK inhibitor PD0325901 (1µM) and GSK3 inhibitor CHIR99021 (3µM) in presence of LIF.
Growth protocol All cell-culture was conducted in feeder-free condition.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina's instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Illumina Casava software 1.8.2 used for basecalling of Hiseq2000 and NextSeq 500 data.
Library strategy: ChIP-seq. The reads were aligned to build version mm9 of the mouse genome using bwa (version 0.7.12) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version, was used to identify regions of ChIP-seq enrichment over background using parameters --nomodel --broad.
Genome_build: mm9
Submission date Aug 18, 2015
Last update date May 15, 2019
Contact name Shuang-Yin Wang
Organization name RIMLS
Department Molecular Biology
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platform ID GPL19057
Series (1)
GSE72164 Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency
BioSample SAMN03998789
SRA SRX1158309

Supplementary file Size Download File type/resource 370.8 Mb (ftp)(http) BW
GSM1856450_Suz12_broad_merged_2i_8468.mem.sorted.q60.rmdup.count.bedGraph.gz 69.3 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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