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| Status |
Public on Mar 23, 2024 |
| Title |
BULK-TCRb_COH4_84 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: T cells
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| Treatment protocol |
FACS sorting for scRNAseq
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| Growth protocol |
none
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| 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
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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.
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| Submission date |
Nov 28, 2023 |
| Last update date |
Mar 23, 2024 |
| Contact name |
Anne-laure Le gac |
| E-mail(s) |
annelaure.legac@gmail.com
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| Phone |
0630777988
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| Organization name |
Institut Curie
|
| Department |
U932
|
| Lab |
Olivier Lantz
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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 (1) |
| GSE248838 |
Divergent local and systemic antitumor response in primary uveal melanomas |
|
| Relations |
| BioSample |
SAMN38474575 |
| SRA |
SRX22665874 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7921151_TCRb-PBMC-UM84_clones_TRB.tsv.gz |
5.9 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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