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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 01, 2013 |
| Title |
KDM5C_ChIP_ES |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
cell type: BirA-expressing IB10 (E14 ES cell subline)
genotype/variation: transfected with tagged Kdm5c transgenic BAC
chip antibody: streptavidin
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| 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 (http://bacpac.chori.org). 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.
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| 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)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 1
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| Data processing |
jarid1cES-R2w200d4Norm10backg8RatioNCSAR_t2.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
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| Submission date |
Jan 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard van Schaik |
| Organization name |
UMCUtrecht
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| Department |
Molecular Cancer Research
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| Street address |
Universiteitsweg 100
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| City |
Utrecht |
| ZIP/Postal code |
3584 CG |
| Country |
Netherlands |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE34975 |
The Kdm5c histone demethylase controls enhancer and promoter function. |
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| Relations |
| SRA |
SRX115144 |
| BioSample |
SAMN00771390 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM859660_jarid1cES-R2w200d4Norm10backg8RatioNCSAR_t2.wig.gz |
1.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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