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GEO help: Mouse over screen elements for information. |
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Status |
Public on Oct 13, 2016 |
Title |
Sample_167_1_K27Ac |
Sample type |
SRA |
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Source name |
splenic B220+ lymphocytes
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Organism |
Mus musculus |
Characteristics |
cell type: lymphoma cells genotype/variation: Crebbp wild-type chip antibody: H3K27Ac (ab4729, Rabbit, 2 ug)
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Growth protocol |
Cells were isolated from mouse spleens upon sacrifice.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin was sheared to 200-400bp, incubated with H3K27ac antibody (abcam 4729) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr. Final chormatin was purified using Qiagen PCR purification columns. Libraries were prepared using the Illumina Truseq ChIPseq Library preparation Kit following the manufacture’s instructions (Illumina, CA).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
H3K27Ac ChIP in mouse cells with scramble shRNA control 167_1
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Data processing |
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis. Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser Genome_build: mouse mm10 build Supplementary_files_format_and_content: bigwig and bigbed formats
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Submission date |
Mar 28, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Huimin Geng |
E-mail(s) |
huimin.geng@ucsf.edu
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Organization name |
UCSF
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Department |
Department of Laboratory Medicine
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Street address |
513 Parnassus Ave., MSB S-1480
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City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94143 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (2) |
GSE79640 |
Loss of CREBBP results in H3K27ac loss at enhancers in mouse lymphoma cells |
GSE79686 |
Loss of CREBBP results in H3K27Ac loss at enhancers and gene expression repression in lymphoma cells |
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Relations |
BioSample |
SAMN04588234 |
SRA |
SRX1665955 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2100304_Sample_167_1_K27Ac_peaks.bigbed |
382.9 Kb |
(ftp)(http) |
BIGBED |
GSM2100304_Sample_167_1_K27Ac_reads.bw |
148.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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