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Sample GSM2100303 Query DataSets for GSM2100303
Status Public on Oct 13, 2016
Title Sample_167_1_Input
Sample type SRA
 
Source name splenic B220+ lymphocytes
Organism Mus musculus
Characteristics cell type: lymphoma cells
genotype/variation: Crebbp wild-type
chip antibody: NA
Growth protocol Cells were isolated from mouse spleens upon sacrifice.
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).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description input DNA for H3K27Ac ChIP in mouse cells with scramble shRNA control 167_1
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
 
Submission date Mar 28, 2016
Last update date May 15, 2019
Contact name Huimin Geng
E-mail(s) huimin.geng@ucsf.edu
Organization name UCSF
Department Department of Laboratory Medicine
Street address 513 Parnassus Ave., MSB S-1480
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
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
Relations
BioSample SAMN04588233
SRA SRX1665954

Supplementary file Size Download File type/resource
GSM2100303_Sample_167_1_Input_reads.bw 196.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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