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Sample GSM1633873 Query DataSets for GSM1633873
Status Public on Jun 12, 2015
Title JB7 H3K27ac_ChIPSeq
Sample type SRA
 
Source name Neutrophil, Chromatin IP against H3K27ac
Organism Homo sapiens
Characteristics cell type: Neutrophil
condition: healthy
chip antibody: Rabbit polyclonal to Histone H3 (acetyl K27) - ChIP Grade (ab4729)
Treatment protocol Whole blood was drawn into 10 mL citrated Cell Preparation Tubes (Becton Dickinson, Franklin Lakes, NJ, USA). Cell separation procedures were started within one hour from the time the specimens were drawn. Peripheral blood mononuclear cells were separated from neutrophils and red blood cells by subjecting the CPT tubes directly to density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis.
Extracted molecule genomic DNA
Extraction protocol Chromatin was fixed in 1% formaldehyde, sheared to 100-900bp using Micrococcal nucleasean (Cell Signalling Technologies Inc.) and ultrasonic sonicator (FB-705, Fisher Scientific), immunoprecipitated using the indicated antibodies, purified and sequenced using Illumina HiSeq 2500 as recommended by the manufacturer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Basecalling : illumina RTA 1.18.64. FASTQ Generation : Casava 1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Alignment ( BWA) with default parameters in bwa aln and bwa samse
peaks were called using MACS version 2 with the following settings:-B --broad --nomodel --extsize 150 -q 0.01 --broad-cutoff 0.1
MACS2 bdgcmp was used to generate fold-enrichment and logLR track with parameters -m FE and -m logLR -p 0.00001
Genome_build: hg19
Supplementary_files_format_and_content: BROADPEAK file reports peaks with FDR q <0.1
 
Submission date Mar 13, 2015
Last update date May 15, 2019
Contact name Lisha Zhu
E-mail(s) lishazhu4508@gmail.com
Organization name UT Health Science Center at Houston
Street address 7000 fannin st
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL16791
Series (2)
GSE66896 Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells [ChIP-Seq]
GSE66898 Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells
Relations
BioSample SAMN03408086
SRA SRX956548

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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