|
| Status |
Public on May 31, 2024 |
| Title |
In_vitro_Multiome_Gene_PBS |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: T cells
treatment: PBS
|
| Growth protocol |
Tumors were collected and digested, and tumor-infiltrating PMEL T cells were enriched and sorted out for scRNA-seq
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
In vivo scRNA-seq was performed using the GEXSCOPE Single Cell RNA Library Kit Cell V2 reagents (Singleron Biotechnologies GmbH). In vitro single-cell ATAC+gene multiome was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics, Cat# PN-1000283)
Libraries were constructed according to the protocols provided by the aforementioned kits.
scRNA-seq and single cell ATAC+Gene multiomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
filtered_feature_bc_matrix.h5
|
| Data processing |
For scRNA-seq, the raw fastq files were generated and demultiplexed by CeleScope rna from Singleron (version 3.0.1) and primary data analysis was performed with CeleScope (version 1.10.0) using a custom reference package based on reference genome (Mus_musculus_ensembl_92)
For ATAC+Gene multiomics, the Cell Ranger ARC v2.0.2 (10x Genomics) was utilized to perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells from the sequenced data.
Assembly: Mus_musculus_ensembl_92
Supplementary files format and content: Gene expression matrix
Supplementary files format and content: Combined Gene+ATAC expression matrix and ATAC fragments and annotation files
|
| |
|
| Submission date |
Feb 27, 2024 |
| Last update date |
May 31, 2024 |
| Contact name |
Rong Fan |
| E-mail(s) |
rong.fan@yale.edu
|
| Organization name |
Yale University
|
| Department |
Biomedical Engineering
|
| Street address |
55 Prospect St.
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE259409 |
A type 2 cytokine Fc–IL-4 revitalises exhausted CD8+ T cells against cancer |
|
| Relations |
| BioSample |
SAMN40178346 |
| SRA |
SRX23771572 |
