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Sample GSM1602246 Query DataSets for GSM1602246
Status Public on Mar 06, 2015
Title RJ2.2.5 ATACseq (paired-end)
Sample type SRA
 
Source name RJ2.2.5 cells
Organism Homo sapiens
Characteristics cell type: RJ2.2.5 cells
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 Briefly, 50,000 cells were FACS sorted into FACS sort buffer (1x PBS, 1 mM EDTA, 1% BSA, 0.25 μM filtered) and processed as described (Buenrostro et al. Nat Methods. 10(12):1213-8 2012). Tagmentation was performed using the Illumina Nextera DNA Sample (FC-121-1030) and Indexing kits (FC-121-1011). Following 10 cycles of PCR amplification, the adaptor ligated DNA was size selected to yield a 200-1,000 bp sequencing library.
See each sample for speicific extract protocols
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description ATAC-seq
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 GPL16791
Series (1)
GSE52941 CIITA regulated genes in human B cells
Relations
BioSample SAMN03329469
SRA SRX865424

Supplementary data files not provided
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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