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Sample GSM859665 Query DataSets for GSM859665
Status Public on Apr 01, 2013
Title H3K4me1_ChIP_sh non targeting
Sample type SRA
Source name embryonic stem cells
Organism Mus musculus
Characteristics strain: 129/Ola
cell type: IB10 (E14 ES cell subline)
chip antibody: H3K4me1
chip antibody vendor: Diagenode
chip antibody cat #: pAB-037-05
Growth protocol IB10 (E14 ES) and its derivative BirA mouse embryonic stem cells were cultured on gelatin-coated dishes in high glucose (4.5 g/l) DMEM (Gibco) media supplemented with 15% Fetal bovine serum, 100 µg/ml Pen/Strep, 2 mM L-glutamine, 100 µM β-mercaptoethanol, 1 mM natrium pyruvate, 100 µM non-essential amino acids and leukemia inhibitory factor (LIF). A Kdm5c containing BAC (RP23-391D18) was obtained from BACPAC Resources Center ( The triple tag V5-FLAG-BIO cassette was inserted as a C-terminal in-frame fusion using bac recombineering (Ciotta, 2011), details available upon request. BirA ES cells were transfected with the recombineered Kdm5c BAC using Lipofectamine 2000 (Invitrogen) and selected on geneticin (G418 sulphate, Gibco). BirA and transgenic derivatives containing the tagged Kdm5c transgenic BAC were differentiated into NPC cells using the procedure described in Conti et al.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina's instructions accompanying the ChIP Seq Sample preparation Kit (Part# IP-102-1001)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Sample 6
Data processing H3K4me1_w200Rawreads_t10.wig; genome build: mm9
Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR
Submission date Jan 10, 2012
Last update date May 15, 2019
Contact name Richard van Schaik
Organization name UMCUtrecht
Department Molecular Cancer Research
Street address Universiteitsweg 100
City Utrecht
ZIP/Postal code 3584 CG
Country Netherlands
Platform ID GPL13112
Series (1)
GSE34975 The Kdm5c histone demethylase controls enhancer and promoter function.
SRA SRX115149
BioSample SAMN00771395

Supplementary file Size Download File type/resource
GSM859665_H3K4me1_w200Rawreads_t10.wig.gz 332.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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