|
| Status |
Public on Oct 06, 2023 |
| Title |
Stomach-IEL |
| Sample type |
SRA |
| |
|
| Source name |
intraepitehlial lymphocytes (IELs)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Stomach
cell type: Live CD45+ cells
infection: None
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
IELs were extracted from mice colons and sorted CD45.2+ leukocytes were then loaded onto to the 10X ChromiumTM Single Cell 3’ Chip to be encapsulated forming Gel Beads in Emulsion (GEM) and cDNA was generated as per 10X genomics protocol.
Single cell RNA sequencing libraries were prepared according to 10X Genomics protocol and using the ChromiumTM Single Cell 3’ Library and Gel Bead Kit (v2)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw 10x Chromium scRNA-seq data were quantified using the cellCounts function in Bioconductor package Rsubread (ver 2.3.6). Sequencing reads were mapped to the GRCm38/mm10 reference genome. Mapped reads were deduplicated and counted to the NCBI mouse RefSeq genes (build 38.1) to produce unique molecular identifier (UMI) counts for each gene in each cell. Genes that failed to express in at least three cells in at least one sample were excluded from analysis. An expressed gene in a cell has at least one UMI count. Mitochondrial genes, ribosomal genes and genes with no known symbols were all excluded from analysis. Cells were excluded from analysis if they expressed < 200 genes or > 2500 genes, or had > 20% of mitochondrial gene content, or had > 40% of ribosomal gene content. Seurat (version 3.0.0) was used to perform t-distributed stochastic neighbour embedding (t-SNE) dimension reduction and unsupervised cell clustering.
The unsupervised cell clustering was performed by using shared nearest neighbour (SNN) modularity optimisation with a resolution parameter of 0.5 and nearest neighbour number of 20.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)
|
| |
|
| Submission date |
May 10, 2022 |
| Last update date |
Oct 06, 2023 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi@onjcri.org.au
|
| Organization name |
Olivia Newton John Cancer Research Institute
|
| Department |
Bioinformatics and Cancer Genomics
|
| Street address |
Level 5, ONJ Cancer Centre, 145 Studley Rd
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE202690 |
Single cell gene expression analysis of mouse CD45.2+ intraepithelial lymphocyes (IELs) from stomach, small intestine, cecum and colon. |
| GSE202692 |
Colorectal cancer |
|
| Relations |
| BioSample |
SAMN28180013 |
| SRA |
SRX15226357 |
