|
| Status |
Public on Feb 19, 2024 |
| Title |
KO_CD4 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
cell type: thymocyte
genotype: PD-1 knockout
strain: C57BL/6J
age: 3 wks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thymi from 4 WT or PD-1 knockout animals were harvested and pooled. Thymi were disrupted with a 1-cc syringe plunger through a 70 um nylon cell strainer and filtered to obtain single-cell suspensions using FACS Buffer (PBS containing 2% FBS and 0.01% sodium azide). CD8+ cells were depleted using CD8a-biotin and rapid spheres followed by a second depletion with CD8b-biotin and rapid spheres, which resulted in enrichment of CD4+ thymocytes. Cells were stained with LIVE/DEAD fixable Aqua followed by extracellular staining with HSA, CD25, CD74, CD4, and CD8a. Cells were resuspended for sorting in FACS buffer and sorted on an Aria (BD Biosciences) using an 85-micron nozzle. Live cells were identified and then the following two populations were sorted: CD4+ HSA+ CD73- CD25- (CD4 single positive thymocytes) and CD4+ HSA+ CD73- CD25+ (regulatory T cells and CD25+ regulatory T cell progenitors) for RNA extraction.
Library preparation was performed according to manufacturer's protocol (Next GEM Single Cell 5' Reagent Kit v2).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics
SCL211022AM_KO_CD4
|
| Data processing |
barcoded processing, gene counting, and aggregation were performed with CellRanger v6.2.1
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files
|
| |
|
| Submission date |
Feb 13, 2024 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Amy E Moran |
| Organization name |
Oregon Health & Science University
|
| Department |
Department of Cell, Developmental & Cancer Biology
|
| Lab |
Moran
|
| Street address |
3181 SW Sam Jackson Park Rd, Mail code KR-CDCB
|
| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE255727 |
PD-1 restrains thymic IL-2 production and regulatory T cell development |
|
| Relations |
| BioSample |
SAMN39938028 |
| SRA |
SRX23616547 |
