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GEO help: Mouse over screen elements for information. |
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Status |
Public on Aug 12, 2015 |
Title |
Rbp2 WT_H3K4me3_ChIPSeq |
Sample type |
SRA |
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Source name |
Rbp2 f/f ES cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 genotype/variation: Rbp2 f/f wild type cell type: embryonic stem cells chip antibody: Anti-trimethyl-Histone H3 (Lys4) chip antibody vendor: Upstate Tech chip antibody cat. #: 07-473
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Treatment protocol |
None
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Growth protocol |
Wild-type (Rbp2 f/f) and Rbp2-/- (Rbp2 KO) ES cells were maintained on irradiated mouse embryonic fibroblast (IEF) feeders in standard ES medium (DMEM; Dulbecco's modified Eagle's medium) supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 1000U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and antibiotics. For ChIP assays, the cells were seeded on gelatin-coated plates.
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Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101). After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~320 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
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Description |
Chromatin IP against H3K4me3
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Data processing |
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained. Peaks: Peak/significant island detection was performed with the program SICER (http://home.gwu.edu/~wpeng/Software.htm) Genome Build: H3K4me3_mmuES_ff_map-mm9.bed: mm9 H3K4me3_ff_mm9_ES.wig: mm9 H3K4me3_mmuES_ff_island.bed: mm9
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Submission date |
Jan 30, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Elizaveta V Benevolenskaya |
E-mail(s) |
evb@uic.edu
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Phone |
312-413-8947
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Organization name |
University of Illinois at Chicago
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Department |
Biochemistry and Molecular Genetics
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Street address |
900 S. Ashland Ave.
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City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60607 |
Country |
USA |
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Platform ID |
GPL9185 |
Series (1) |
GSE28348 |
Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells. |
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Relations |
SRA |
SRX118195 |
BioSample |
SAMN00779770 |
Supplementary file |
Size |
Download |
File type/resource |
GSM867826_H3K4me3_ff_mm9_ES.wig.gz |
279.2 Mb |
(ftp)(http) |
WIG |
GSM867826_H3K4me3_mmuES_ff_island.bed.gz |
319.2 Kb |
(ftp)(http) |
BED |
GSM867826_H3K4me3_mmuES_ff_map-mm9.bed.gz |
228.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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