|
| Status |
Public on Jan 16, 2024 |
| Title |
Synovial ILCs, R5 healthy mice gene expression library |
| Sample type |
SRA |
| |
|
| Source name |
synovial ankle/wrist joints
|
| Organism |
Mus musculus |
| Characteristics |
cell type: synovial cells
tissue: synovial ankle/wrist joints
strain: R5 x R26tdTomato
genotype: Il5 wt/Cre; R26 tdTom/tdTom
treatment: untreated
library type: mRNA
antibodies/tags: none
age: 8-10 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted and purified cells were stained for 30 min on ice in PBS containing 1 % (w/v) BSA with hashtag antibodies (TotalSeq-B0301/B0302/B0303/B0304B0305 anti- mouse Hashtag 1/2/3/4/5, respectively, Biolegend). Cells were washed, counted and concentrated to 1,000 cells / µl prior to pooling.
Up to 25,000 cells (hyper-loading) pooled from 4 animals were loaded into a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev D). Libraries were sequenced as PE150 by Illumina sequencing to 65-80% saturation by the external provider Novogene.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
R5_STA_r1_ILCs_HC_barcodes.tsv.gz
R5_STA_r1_ILCs_HC_features.tsv.gz
R5_STA_r1_ILCs_HC_matrix.mtx.gz
|
| Data processing |
The barcoded processing, gene counting and HTO processing were made using the Cell Ranger software v6.0.6
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Apr 04, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Hashem Mohammadian |
| Organization name |
University of Erlangen-Nürnberg
|
| Department |
Department of Medicine 3 - Rheumatology and Immunology
|
| Street address |
Ulmenweg 18
|
| City |
Erlangen |
| ZIP/Postal code |
91054 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE228980 |
Molecular reframing of fibroblasts during resolution of arthritis [scRNA] |
| GSE228982 |
Molecular reframing of fibroblasts during resolution of arthritis |
|
| Relations |
| BioSample |
SAMN34072223 |
| SRA |
SRX19868689 |
