|
Status |
Public on Feb 19, 2024 |
Title |
Mock |
Sample type |
SRA |
|
|
Source name |
murine tumor infiltration lymphocytes
|
Organism |
Mus musculus |
Characteristics |
strain/background: C57BL/6 tissue: B16 Pten-/- tumor cell type: tumor infiltrating lymphocytes treatment: 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.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
10x scRNA-Seq
|
Data processing |
The Cell ranger software pipeline (version 5.0.0) provided by 10x Genomics 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 UMI numbers greater than 3000 or less than 300, or having over 10% 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 (GRCm38) Supplementary_files_format_and_content: features.tsv: gene files; barcodes.tsv: cell barcode files; matrix.mtx: gene-barcode counts.
|
|
|
Submission date |
Feb 24, 2021 |
Last update date |
Feb 19, 2024 |
Contact name |
Yizhe Sun |
E-mail(s) |
sunyz1105@bjmu.edu.cn
|
Phone |
+8615811526996
|
Organization name |
Peking University Health Science Center
|
Street address |
No.38, Xueyuan Road ,Haidian District
|
City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100191 |
Country |
China |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE167469 |
PTENĪ± functions as an immune suppressor and promotes immune resistance in PTEN-mutant cancer |
|
Relations |
BioSample |
SAMN18053069 |
SRA |
SRX10165410 |