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Sample GSM4952980 Query DataSets for GSM4952980
Status Public on Jan 29, 2021
Title P61 Juxta
Sample type SRA
 
Source name NSCLC juxta tissue
Organism Homo sapiens
Characteristics tumor stage: NA
tissue: NSCLC juxta tissue
smoking status: NA
tumor type: NA
Sex: M
Treatment protocol Tumor and adjacent normal lung tissue samples were gently cut in approximately 1mm3 pieces. Tissues were digested enzymatically, by an incubation of 20-40 minutes, based on the size of the tissue, at 37oC in agitation, in C02-independent medium (Invitrogen) with Collagenase I (2mg/ml, Sigma-Aldrich), Hyaluronidase (2mg/ml, Sigma-Aldrich) and DNase (25μg/ml, Sigma-Aldrich). The tissue pieces were gently triturated with a 20 ml syringe plunger on a 40 μ m cell strainer (BD) in 1X PBS (Invitrogen) with 1% fetal bovine serum (FBS) and 2mM EDTA (Gibco) until uniform cell suspensions were obtained. The suspended cells were subsequently centrifuged for 10 minutes at 400g and resuspended in PBS 1X buffer with 1% FBS and 2mM EDTA (Gibco). Isolation of tumor infiltrating lymphocytes and peripheral blood mononuclear cells was performed using Ficoll-paque PLUS solution (Sigma-Aldrich). CD3+ T cell isolationwas performed using CD3 microbeads and MACS separation (Miltenyi). Susequently dead cells and debris was removed following SOP (Dead cell removal kit; Debris removal kit; Miltenyi Biotec). Purified CD3+ T cells were resuspended in 1X PBS buffer with 0.04% BSA.
Extracted molecule total RNA
Extraction protocol TCR libraries from P47, P55, P57, P58 and P61 was extracted according to the Single Cell VDJ 5' Reagent Kits
TCR enrichment from amplified cDNA
5' for paired single cell TCR-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v2.0.1) and with for and (v3.0.2) for P57, P58, P60 and P61.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are filtered contigs annotations files which are given by Cellranger pipeline.
 
Submission date Dec 02, 2020
Last update date Jan 29, 2021
Contact name Paul Gueguen
E-mail(s) paul.gueguen@unil.ch
Organization name Institut Curie
Department Inserm U932
Street address 26 rue D'Ulm
City Paris
ZIP/Postal code 75005
Country France
 
Platform ID GPL24676
Series (2)
GSE162499 Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer [scTCR-seq]
GSE162500 Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer
Relations
BioSample SAMN16979802
SRA SRX9619523

Supplementary file Size Download File type/resource
GSM4952980_P61_Juxta_filtered_contig_annotations.csv.gz 76.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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