|
| Status |
Public on May 17, 2024 |
| Title |
Mouse neonate thymocytes, Mock infected |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
cell type: neonate thymocytes
treatment: mock (saline) infected
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The thymus was dissected with care to remove non-thymic tissue using scissors. The thymus tissue was placed into 1ml of 0.25% trypsin EDTA (GIBCO) at 37ºC. The tissue was incubated for 15 minutes. Dissociation and digestion were aided by vigorous pipetting using a large bore pipette every 5 minutes. Cells were filter through a 100μm filter into 9ml of RPMI 10% FBS to neutralize trypsin activity. Cells were then centrifuged at 1500rpm for 3.5 minutes followed by incubation in RBC lysis buffer (made in house) for 3 min at room temperature. Cells were then centrifuged again and washed twice in 9ml of PBS 0.5% bovine serum albumin (BSA). Cells were counted via hemocytometer then resuspended at 1200 cells/μL in PBS 0.04% BSA. The cells were kept on ice until ready for scRNAseq analysis.
Single-cell 3’ gene expression cDNA libraries were generated per manufacture protocols using the 10X Genomic Chromium Single-Cell 3’ Library and Gel Bead Kit v1 and the 10x Chromium Controller
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Cell Ranger v3.1.0 Pipeline
Assembly: A custom refernce genome combining GRCm38 with the murine roseolovirus genome
Supplementary files format and content: compressed tab-delimited text file contains raw counts
Supplementary files format and content: compressed tab-delimited text file contains barcodes
Supplementary files format and content: compressed tab-delimited text file contains features
|
| |
|
| Submission date |
Feb 13, 2024 |
| Last update date |
May 17, 2024 |
| Contact name |
Andrei Belean |
| E-mail(s) |
belean@wustl.edu
|
| Organization name |
Washington University in Saint Louis
|
| Department |
IM-Rheumatology
|
| Lab |
Paley Lab
|
| Street address |
4939 Children’s Place
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE255738 |
Transcriptomic profiling of thymic dysregulation and viral tropism after neonatal roseolovirus infection |
|
| Relations |
| BioSample |
SAMN39938273 |
| SRA |
SRX23616793 |
