|
| Status |
Public on Dec 27, 2018 |
| Title |
Rptor KO rep1 (scRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Rptor KO, spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: TCRb+YFP+ cells
age: 6-10 weeks
genotype: Rptorll17aCre
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were immunized with MOG. TCRb+YFP+ cells from spleen at day 9 post-immunization sorted on an iCyt Reflection cell sorter. The cells were counted and examined for viability using a Luna Dual Florescence Cell Counter (Logos Biosystems). All samples were spun down at 2,000 rpm for 5 min. The supernatant was removed, and cells were re-suspended in 100 ul of 1× PBS (Thermo Fisher Scientific) + 0.04% BSA (Amresco)
Single-cell suspensions were loaded onto the Chromium Controller according to their respective cell counts to generate 6000 single cell GEMs (gel beads in emulsion) per sample. Libraries were prepared using the Chromium Single Cell 3’ v2 Library and Gel Bead Kit (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The Cell Ranger 1.3 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Dec 27, 2018 |
| Contact name |
Hongbo Chi |
| E-mail(s) |
hongbo.chi@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Immunology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE121598 |
Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity [scRNA-seq] |
| GSE121599 |
Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity |
|
| Relations |
| BioSample |
SAMN10267487 |
| SRA |
SRX4912142 |
