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| Status |
Public on Jun 24, 2024 |
| Title |
4041 NP cells, scTCRseq biol rep 2 |
| Sample type |
SRA |
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| Source name |
nasopharynx
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| Organism |
Homo sapiens |
| Characteristics |
tissue: nasopharynx
library type: TCR
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| 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
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Jun 24, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Shane Crotty |
| Organization name |
La Jolla Institute for Immunology
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| Street address |
9420 Athena Circle
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE270518 |
Immunological memory diversity in the human upper airway |
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| Relations |
| BioSample |
SAMN42007230 |
| SRA |
SRX25040305 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8345891_1_TCR_4041_CR-NS_2_filtered_contig.fasta.gz |
583.7 Kb |
(ftp)(http) |
FASTA |
| GSM8345891_1_TCR_4041_CR-NS_2_filtered_contig_annotations.csv.gz |
783.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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