|
| Status |
Public on Oct 25, 2023 |
| Title |
MWIK_2 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
cell type: medullary thymic epithelial cell
genotype: Foxn1-Cre(+) Ikarosfl/fl
|
| Treatment protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly sorted EPCAM+Ly51- mTECs were collected in 0.04% BSA in PBS, then sent to the UCSF Genomics core for processing
Per UCSF Genomics Core
Single cells were captured using the 10X Chromium microfluidics system and cells were encapsulated and barcoded cDNA libraries were prepared using the single-cell 3'mRNA kit (10X Genomics). Single cell libraries were sequenced using a NovaSeq 6000 (lllumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQ files were converted into single cell matrices using 10X Cell Ranger and were transformed into a Seurat object using the Seurat package in R
Initial exclusion criteria included features that were present in less than 100 cells and cells where less than 1000 features were detected
|
| |
|
| Submission date |
Aug 25, 2023 |
| Last update date |
Oct 25, 2023 |
| Contact name |
Jun Hyung Sin |
| E-mail(s) |
junhyung.sin@ucsf.edu
|
| Phone |
4242419276
|
| Organization name |
University of California, San Francisco
|
| Department |
Pediatrics
|
| Lab |
Waterfield
|
| Street address |
513 Parnassus Ave S-1076
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE241742 |
Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance (scRNA seq) |
|
| Relations |
| BioSample |
SAMN37166182 |
| SRA |
SRX21496062 |
