|
| Status |
Public on Mar 15, 2024 |
| Title |
P14 T cells sorted from B16-OVA tumor treated with PBS, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
P14_T_cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: P14_T_cells
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were loaded into microfluidic devices and scRNA-seq libraries were constructed following the Singleron GEXSCOPER protocol by GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies).
Indivaidual libraries of each sample were then dilyted to 4nM, pooled and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Singleron Matrix GEXSCOPE
PBS_P14_2
|
| Data processing |
The demultiplexing, barcoded processing, alignment, gene counting and aggregation were made using the Singleron Celescope software version 1.10.0 (https://github.com/singleron-RD/CeleScope)
The doublet were removed by using Doubletfinder R package and personal checking for conserved markers.
The R package Seurat version 4.1.1 was used for normalization, clustering and reduction. Cell type was annotated based on conserved markers.
Differential gene expression analysis and enrichment analysis were performed by using MAST and clusterProfiler R package.
Assembly: GRCm38
Supplementary files format and content: Compressed .tar.gz file containing genes, barcodes and matrix for each sample
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Mar 15, 2024 |
| Contact name |
Jinhang He |
| E-mail(s) |
hejinhang@stu.xmu.edu.cn
|
| Phone |
15821251893
|
| Organization name |
Xiamen University
|
| Street address |
No.4221, South Xiang'an Road
|
| City |
Xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361104 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE235290 |
Combination therapy with oncolytic virus and adoptively transferred T cells or mRNA vaccine amplifies antitumor effects [scRNA-Seq] |
| GSE235291 |
Combination therapy with oncolytic virus and adoptively transferred T cells or mRNA vaccine amplifies antitumor effects |
|
| Relations |
| BioSample |
SAMN35813328 |
| SRA |
SRX20732281 |
