 |
 |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 19, 2024 |
Title |
Mock |
Sample type |
SRA |
|
|
Source name |
murine tumor infiltration lymphocytes
|
Organism |
Mus musculus |
Characteristics |
strain: BALB/c tissue: tumor genotype: mock
|
Extracted molecule |
total RNA |
Extraction protocol |
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification. RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol. 10x scRNA-Seq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix. The R package Seurat (version 3.2.3) was used for generation of Seurat object. Low-quality cells with over 15% mitochondrial-derived UMI counts were removed. The count matrix was normalized with SCTransform function. IntegrateData function was used to integrate data and create a new matrix with 3000 features. PCA was performed by R package Seurat (version 3.2.3). Top 40 PCs were used for tSNE and UMAP. tSNE and UMAP were performed by R package Seurat (version 3.2.3). Genome_build: mm10 Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.
|
|
|
Submission date |
Mar 14, 2021 |
Last update date |
Feb 19, 2024 |
Contact name |
Jia Song |
E-mail(s) |
songjia@bjmu.edu.cn
|
Phone |
+18830053918
|
Organization name |
Peking University
|
Street address |
Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing
|
City |
Beijing |
State/province |
China |
ZIP/Postal code |
100080 |
Country |
China |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE168862 |
PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance |
|
Relations |
BioSample |
SAMN18306508 |
SRA |
SRX10338557 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5171679_1_barcodes.tsv.gz |
53.5 Kb |
(ftp)(http) |
TSV |
GSM5171679_1_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
GSM5171679_1_matrix.mtx.gz |
72.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
 |