|
| Status |
Public on Apr 09, 2024 |
| Title |
scRNA-seq HTO library, T cells, lane1 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: skin
cell type: T cells
genotype: WT male and female
treatment: Control and S. epidermidis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skin lymphocytes (CD45+ Thy1.2+, exclude γδTCRhi population) or skin dendritic cells (CD45+ Lin- Ly6G- Siglec-F- CD11c+ MHC-II+) from 8-9-week-old female and male mice were sorted from samples labeled with TotalSeqC hashtags antibodies (BioLegend) on a Sony MA900 cell sorter.
10X Genomics 5' kit
All DC and all T cell samples were pooled together in two separate vials, and 45,000 cells were loaded to a Chromium Single Cell Controller (10X Genomics) to encapsulate cells into droplets. Libraries were prepared using a Chromium Single Cell 5’ Reagent Kit (10X Genomics) following manufacturer's instructions and the HTO library was prepared according to a previous publication (M. Stoeckius et al, 2019). Libraries were then sequenced on an Illumina Nextseq500 (Next Seq 500/550 High Output Kit v2, Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HTO_features_Tcells.csv
Tcells_lane1_matrix.mtx.gz
Tcells_lane1_features.tsv.gz
Tcells_lane1_barcodes.tsv.gz
Tcells_SeuratObj.rds
|
| Data processing |
Data were filtered and mapped to mm10 reference genome by using Cellranger 6.1.1 (10X Genomics). Data were normalized in Seurat.
Assembly: mm10
Supplementary files format and content: csv files for HTO libraries to run cellranger count
Supplementary files format and content: csv files for features and barcodes - output of cellranger count
Supplementary files format and content: mtx files for count matrix - output of cellranger count
Supplementary files format and content: rds files for Seurat objects
|
| |
|
| Submission date |
Jan 15, 2024 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Verena Link |
| E-mail(s) |
[email protected]
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Street address |
4 Memorial Drive
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE253294 |
Sexual dimorphism in skin immunity is mediated by androgen-ILC2-dendritic cell axis [scRNA-seq] |
| GSE253295 |
Sexual dimorphism in skin immunity is mediated by androgen-ILC2-dendritic cell axis |
|
| Relations |
| BioSample |
SAMN39447788 |
| SRA |
SRX23223855 |
