|
| Status |
Public on May 16, 2022 |
| Title |
sc-RNAseq of CD4conv and Treg cells in BM and spleen |
| Sample type |
SRA |
| |
|
| Source name |
T cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: multiplexed sample: Spleen and bone marrow
cell type: multiplexed sample: Tregs and CD4 conv
age: 9 weeks
genotype: Foxp3DTR-GFP
|
| Treatment protocol |
The mice were not treated before the experiment (WT mice)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspension from BM and spleen were prepared, enriched for CD4, sorted by gating on CD4+TCRb+GFP+ (Tregs) and CD4+TCRb+GFP- (CD4conv) and hashtagged.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Alignment of fastq files
Gene quantification
Incorporate hashtag information
Filtering, normalization and log transformation
tSNE and clustering
Assembly: GRCm38
Supplementary files format and content: norm_df_all_samples.txt: cellXgene full table
Supplementary files format and content: norm_df.txt: cellXgene table for BM Treg cells
Supplementary files format and content: clusters.txt: clusters for BM Treg cells
|
| |
|
| Submission date |
May 12, 2022 |
| Last update date |
May 17, 2022 |
| Contact name |
Michail Schizas |
| E-mail(s) |
schizasm@mskcc.org
|
| Organization name |
Memorial sloan Kettering
|
| Street address |
1275 York ave
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE202888 |
scRNA-seq to study features of CD4conv and Treg cells in spleen and bone marrow of mice |
|
| Relations |
| BioSample |
SAMN28207924 |
| SRA |
SRX15244329 |
