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Sample GSM1602241 Query DataSets for GSM1602241
Status Public on Mar 06, 2015
Title Raji H3K4me3
Sample type SRA
 
Source name Raji cells
Organism Homo sapiens
Characteristics cell type: Raji cells
chip antibody: H3K4me3 (Millipore, 07-473)
Growth protocol Raji and RJ2.2.5 cells were cultured in RPMI supplemented with 5% FCS, 5% FBS, and 100 U/ml Penecillin/Streptomycin
Extracted molecule genomic DNA
Extraction protocol 10 ng of Raji H3K4me3 ChIP DNA was processed into a sequencing library using teh Bioo Scientific NEXTflex ChIP-seq kit (Cat# 5143-01) according to the manufacturers instructions.
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717). Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp. 30 mg chromatin was immunoprecipitated with 5 μg anti-CIITA, anti-H3K27ac or anti-H3K4me3 antibody over night at 4 degrees. Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified. Input fraction was isolated after sonication and prior to the IP.
See each sample for speicific extract protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Raw sequencing reads were mapped to the hg19 version of the mouse genome with Bowtie using the default options
For CIITA ChIPseq peak calling HOMER software (Heinz et al. Mol Cell, 2010. 38:576-589) was used with the options "-style factor"
For ATACseq paired-end and single end fastq files from the same cell type were merged into one bigWig file
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are normalized to reads per million (rpm) using R/Bioconductor. Bed files contain the genomic locations of significantly enriched peaks as determined by HOMER
 
Submission date Feb 04, 2015
Last update date May 15, 2019
Contact name Chris Scharer
E-mail(s) cdschar@emory.edu
Organization name Emory University
Department Microbiology and Immunology
Lab Chris Scharer
Street address 1510 Clifton Rd, Suite 3086A
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL11154
Series (1)
GSE52941 CIITA regulated genes in human B cells
Relations
BioSample SAMN03329460
SRA SRX865419

Supplementary file Size Download File type/resource
GSM1602241_Raji.H3K4me3.bigWig 58.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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