|
| Status |
Public on Jun 12, 2015 |
| Title |
JB8 input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Neutrophil
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neutrophil
condition: healthy
chip antibody: N/A
|
| 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 |
SAMN03408089 |
| SRA |
SRX956552 |
