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Sample GSM6190649 Query DataSets for GSM6190649
Status Public on Jun 03, 2022
Title Patient 5125 10x VDJ Replicate 1
Sample type SRA
 
Source name PBMC
Organism Homo sapiens
Characteristics individual: Patient 5125
age: 34
Sex: Male
hiv-1 infected: Yes
aviraemic: Yes
art: Yes
tissue: PBMC
cell type: CD4+ T cells
library type: VDJ RNA
Extracted molecule polyA RNA
Extraction protocol PBMCs were obtained from HIV-1 infected, aviraemic individuals under ART by leukapheresis and stored on liquid nitrogen. CD4+ CD45RA- cells were isolated by magnetic-activated cell sorting. Cells were subsequently incubated with Fc blocking reagent, and stained with a combination of anti-CD3 and/or anti-CD4, anti-TRBC1, and one or a combination of various anti-TRBV antibodies. Cells were sorted for CD3 and/or CD4, a specific TRBC domain and/or a specific TRBV domain or a subset of various TRBV domains.
Library was performed according to the manufacter’s instructions (single cell 5’ and V(D)J Enrichment v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model NextSeq 550
 
Description 5' VDJ library: read1 file contains cell barcode and UMI; read2 file contains transcript
Data processing The demultiplexing, barcoded processing, TCR assembly and gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, VDJ_filtered_contig_annotations.csv
Library strategy: VDJ-seq
 
Submission date May 24, 2022
Last update date Jun 03, 2022
Contact name Thiago Y Oliveira
E-mail(s) toliveira@rockefeller.edu
Organization name The Rockefeller University
Department Immunology, Virology and Microbiology
Lab Laboratory of Molecular Immunology
Street address 1230 YORK AVE
City NEW YORK
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL21697
Series (1)
GSE204756 Distinct gene expression by expanded clones of quiescent memory CD4+ T cells harboring intact latent HIV-1 proviruses
Relations
BioSample SAMN28647798
SRA SRX15446289

Supplementary file Size Download File type/resource
GSM6190649_5125_10x_01_VDJ_filtered_contig_annotations.csv.gz 1.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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