|
| Status |
Public on Mar 10, 2023 |
| Title |
Tcells_LN_GEX |
| Sample type |
SRA |
| |
|
| Source name |
MedLN
|
| Organism |
Mus musculus |
| Characteristics |
tissue: MedLN
cell type: Lymphocyte
cell subtype: CD4+ and CD8+ T-cells
genotype: C57BL/6
treatment: Aging
age: multiplexed sample: 2, 6, 12, 18 months
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Heart and medistinal lymph nodes were collected from mice from the different age groups and all tissues were kept in HBSS/BSA 0.5% at 4°C until processing. Heart samples were digested in collagenase II 1000U/mL and dispase II 1.2U/ml for 45 minutes, at 37ºC. After digestion, both tissues were grinded through a 30um mesh and seeded in a plate for FACS staining. Each condition was stained with a different Hashtag TotalSeq-C antibodies to enable multiplexing. Gating strategy is defined in the supplemental methods. After sorting, cells were combined at different ratios for single cell RNA sequencing application.
Cells were loaded in the 10X Genomics Chromium with the aim of recovering 12,000 cells. Libraries were generated with the Chromium Next GEM Single Cell 5’ Reagents Kit v2 Chemistry according to manufacturer ´s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GEX library
The file Supplemental table I.xlsx contains the age associated with each Hashtag
LN_T_cells_Aging_Productive_TCRs.Robj
LN_T_cells_Aging.Robj
|
| Data processing |
The sequencing data was processed using CellRanger software (version 3.1.0).
Assembly: mm10 for GEX and GRCm38 for V(D)J
Supplementary files format and content: tsv; gene barcode matrices and feature barcode matrix
Supplementary files format and content: csv; clonotypes and contigs
|
| |
|
| Submission date |
Nov 02, 2022 |
| Last update date |
Mar 10, 2023 |
| Contact name |
Antoine-Emmanuel Saliba |
| E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
|
| Phone |
+49-931-31-81341
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2 / D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE217098 |
An interferon gamma response signature links myocardial aging and immunosenescence |
|
| Relations |
| BioSample |
SAMN31573049 |
| SRA |
SRX18121381 |
