|
| Status |
Public on Nov 22, 2019 |
| Title |
NDN_ctrl_01 [ATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Human whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Healthy (control)
cell type: NDN
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. LDGs were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies.
ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013) with minor modification. 100,000 cells performed in quadruplicate for each sample were treated with the Tn5 transposase (Illumina) for 30 min at 37°C and PCR-purified (Qiagen) to generate library fragments.
ATAC seq data were generated on Illumina HiSeq 2500 instruments according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A01
Exp ID: 151013_0265_s25
|
| Data processing |
Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. PE reads of 50 bases were mapped to the hg19 using Bowtie 1.1.1.
Peak calling: Redundant reads were removed using Fastquniq. Uniquely mapped reads from fragments less than 175 bp were used to call peaks with MACS 2.1.1 using a p-value threshold of 1 x 10-5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files
|
| |
|
| Submission date |
Oct 24, 2019 |
| Last update date |
Nov 22, 2019 |
| Contact name |
Hong-wei Sun |
| Organization name |
NIAMS
|
| Department |
Office of Science & Technology
|
| Lab |
Biodata Mining & Discovery Section
|
| Street address |
9000 Rockville Pile
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE139359 |
Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus [ATAC-seq] |
| GSE139360 |
Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus |
|
| Relations |
| BioSample |
SAMN13109369 |
| SRA |
SRX7052862 |
