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Sample GSM8345907 Query DataSets for GSM8345907
Status Public on Jun 24, 2024
Title 4093 NP cells, scTCRseq biol rep 2
Sample type SRA
 
Source name nasopharynx
Organism Homo sapiens
Characteristics tissue: nasopharynx
library type: TCR
Extracted molecule total RNA
Extraction protocol NP single cell suspensions were subjected to column-based dead cell removal (Miltenyi) then stained with CITE-seq Ab +/- probes before single cells were encapsulated in gel-beads-in emulsion (GEMs) using the 10x controller with a Chromium single cell 5' GEM libray and gel bead kit (v2). Sorted probe-positive memory B cells or AIM+ memory T cells underwent the same 10x processing.
CITE-seq per manufacturer's protocol
scRNA-seq, CITE-seq, scTCR-seq, scBCR-seq
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing CellRanger v6.0 or higher mkfastq and count were used for GEX/CSP to generate a single set of processed files per paired GEX/CSP samples. CellRanger v6.0 or higher vdj used for TCR and BCR sequencing to annotate contigs and call cells.
Filtered CellRanger output files for GEX/CSP were used for Seurat v4.0 (or higher) analysis to determine cell counts, cluster cells by identity, etc.
BCR and TCR sequence analysis was performed using Immcantation or Platypus (TCR), with the cell barcodes used to assign BCR and TCR sequences to cells present in the Seurat object made from the GEX/CSP data.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for GEX/CSP; feature_reference.csv lists CSP features (CITE-seq Ab for samples labeled with TBNK Ab, HTO for hashtag Ab labeled samples, ADT for probe-labeled samples)
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv, filtered_contig.fasta for TCR and BCR sequencing
 
Submission date Jun 24, 2024
Last update date Jun 25, 2024
Contact name Shane Crotty
Organization name La Jolla Institute for Immunology
Street address 9420 Athena Circle
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL24676
Series (1)
GSE270518 Immunological memory diversity in the human upper airway
Relations
BioSample SAMN42007214
SRA SRX25040357

Supplementary file Size Download File type/resource
GSM8345907_2_TCR_4093_CR_NS_2_filtered_contig.fasta.gz 34.2 Kb (ftp)(http) FASTA
GSM8345907_2_TCR_4093_CR_NS_2_filtered_contig_annotations.csv.gz 44.9 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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