|
| Status |
Public on Oct 25, 2022 |
| Title |
SA-NucPr-2_VDJ |
| Sample type |
SRA |
| |
|
| Source name |
Lymph node
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lymph node
strain: C57BL/6
cell type: Follicular T cells
genotype: WT
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single Cell 5' R2-only
Single cell libraries were generated using the 10x Genomics Chromium Controller with Immune Profiling reagents following the manufacturer’s protocol (10x Genomics)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
10x Genomics CellRanger-6.1.2
The single cell RNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 5′ R2 only following the manufacturer’s protocol.
The libraries were run on the PerkinElmer LabChip GX Touch HT for library quality control before sequencing.
Libraries were sequenced on a NovaSeq6000 with the following run configuration: R1 - 28, Index1-10, R2 - 150. The total number of cells recovered was 15514.
mm10
Assembly: comma-separated values file that is a delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: html file containing summary of the processed data
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Oct 28, 2022 |
| Contact name |
Irina Grigorova |
| E-mail(s) |
igrigor@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Microbiology and Immunology
|
| Street address |
1150 W MEDICAL CENTER DR
|
| City |
Ann Arbor |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE216236 |
Gene expression and VDJ TCR profile of follicular T cells from immunized with nuclear proteins and control mice |
|
| Relations |
| BioSample |
SAMN31392788 |
| SRA |
SRX17971671 |
