|
| 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 |
