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Sample GSM7921147 Query DataSets for GSM7921147
Status Public on Mar 23, 2024
Title SCRNAseq_COH4_84
Sample type SRA
 
Source name tumor
Organism Homo sapiens
Characteristics tissue: tumor
cell type: T cells
Treatment protocol FACS sorting for scRNAseq
Growth protocol none
Extracted molecule total RNA
Extraction protocol Trizol for bulk TCR
Human TCR RNA Multiplex-Thrm-001 Kit (MiLaboratories) for bulk TCR,
10X
Other : CITE-seq, bulk TCRseq
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing For the single cells, the demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software version 7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For the bulk TCR seq, Mixcr (version 4.4.2) was used to perform the alignment and assemble the reads with the following parameters: milab-human-rna-tcr-umi-multiplex.
Assembly: GRCh38-2020-A for the scRNA-seq and vdj_GRCh38_alts_ensembl-3.1.0-3.1.0 for sc V(D)J-seq.
 
Submission date Nov 28, 2023
Last update date Mar 23, 2024
Contact name Anne-laure Le gac
E-mail(s) annelaure.legac@gmail.com
Phone 0630777988
Organization name Institut Curie
Department U932
Lab Olivier Lantz
Street address 26 rue d'ulm
City PARIS
ZIP/Postal code 75005
Country France
 
Platform ID GPL24676
Series (1)
GSE248838 Divergent local and systemic antitumor response in primary uveal melanomas
Relations
BioSample SAMN38474579
SRA SRX22665870

Supplementary file Size Download File type/resource
GSM7921147_coh4_84_barcodes.tsv.gz 62.5 Kb (ftp)(http) TSV
GSM7921147_coh4_84_features.tsv.gz 325.7 Kb (ftp)(http) TSV
GSM7921147_coh4_84_matrix.mtx.gz 67.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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