|
| Status |
Public on Mar 29, 2022 |
| Title |
Lesional CD4+ T Cells - Obese Control (wt Bl6) Mice given Control HFD |
| Sample type |
SRA |
| |
|
| Source name |
sorted lesional skin CD4+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
main figures: 3
agent: N/A
diet: High Fat Diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD4+ T cells were sorted via flow cytometry from a single cell suspension of lesional immune cells
Single cell RNA sequencing libraries were prepared with the 10x Genomics Chromium Single Cell 3’ Reagent Kit (v3).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
scRNAseq for single sample
|
| Data processing |
Raw fastqs were aligned to the `refdata-cellranger-mm10-3.0.0` reference provided by 10x Genomics.
Filtering for expressed genes and high-quality cells was performed as described in the publication.
RNA Velocity estimation was performed with Velocyto (v0.17.17) and attached to merged scRNAseq expression matrices in scVelo (v0.2.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered Feature-Barcode Matrices outputted from Cellranger (10x Genomics).
|
| |
|
| Submission date |
Nov 24, 2021 |
| Last update date |
Mar 29, 2022 |
| Contact name |
Alexander Marson |
| Organization name |
Gladstone-UCSF Institute of Genomic Immunology
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE189476 |
Correcting altered immunological responses in obesity restores efficacy of targeted biologic therapy for inflammatory disease |
|
| Relations |
| BioSample |
SAMN23423886 |
| SRA |
SRX13217065 |
