GSM2976428: ATAC SLE413-PD1hi; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA
Attributes by original data submitter
Sample
source_name
Sorted CXCR3+ PD1hi CD4+ T cells from PBMCs of SLE patient
donor
SLE413
diagnosis
systemic lupus erythematosus (SLE)
cell type
CD4+ T cell
cell population
PD1hi
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
For blood CD4+ T cell subset sorting, frozen PBMCs from SLE patients were stained with anti-CD4 PE-Cy7, anti-CXCR5 AlexaFluor 647, anti-CD45RA APC-H7, anti-PD1 Brilliant Violet 421, anti-CD3 V500 and anti-CXCR3 Brilliant Violet 785. CXCR3- PD1hi CD4+ T cells were sorted from the CD3+ CD4+ CD45RA- CXCR5- cells fraction, and Tfh cells (CD3+ CD4+ CD45RA− CXCR5+ CD4+ T cells) were also sorted for comparison. ATAC-seq was performed as previously described (Buenrostro et al., 2013). 20,000 unfixed nuclei were tagged using Tn5 transposase (Nextera DNA sample prep kit; Illumina) for 30 min at 37°C, and the resulting library fragments were purified using a Qiagen MinElute kit. Libraries were amplified by 10–12 PCR cycles, purified using a Qiagen PCR cleanup kit, and sequenced on an Illumina HiSeq 2500 with 75 bp paired-end reads and average depth of 79 million reads per sample.