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Status |
Public on Jan 29, 2021 |
Title |
P61 Juxta |
Sample type |
SRA |
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Source name |
NSCLC juxta tissue
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Organism |
Homo sapiens |
Characteristics |
tumor stage: NA tissue: NSCLC juxta tissue smoking status: NA tumor type: NA Sex: M
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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.
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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.
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Submission date |
Dec 02, 2020 |
Last update date |
Jan 29, 2021 |
Contact name |
Paul Gueguen |
E-mail(s) |
paul.gueguen@unil.ch
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Organization name |
Institut Curie
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Department |
Inserm U932
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Street address |
26 rue D'Ulm
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City |
Paris |
ZIP/Postal code |
75005 |
Country |
France |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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