|
Status |
Public on Feb 08, 2021 |
Title |
H8 |
Sample type |
SRA |
|
|
Source name |
24-month-old
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL6/J sorting antibodies: CD45highCD8+
|
Extracted molecule |
total RNA |
Extraction protocol |
Blood was rinsed with PBS containing heparin; brains were dissected, collected in ice‐cold PBS, and cut into small pieces. Tissue was digested in 1 ml Accutase (Merck) per brain at 37 °C for 30 min and triturated through 100 μm cell strainers which were rinsed with 10% FCS in PBS. Cells were purified by a linear 40% Percoll (GE Healthcare) centrifugation step at 650 xg without brakes for 25 min and the myelin top layer and supernatant were discarded. Mononuclear cells were resuspended in FACS buffer (1% BSA and 0.1% sodium azide in PBS) and counted. For scRNA-seq cells from brains of 5 12-month-old and 4 24-month-old mice were pooled into 2 separate samples. Around 15,000 CD45highCD8+ single-cells were sorted per sample and encapsulated in droplets using 10X Genomics GemCode Technology kit v2 and processed following manufacturer’s specifications. Chromium single cell 3´ v2 (10XGenomics)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Data were analyzed using Cell Ranger™ v2.0.2 pipelines which is available in 10xGenomics website. Genome_build: mm10 Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
|
|
|
Submission date |
Oct 15, 2019 |
Last update date |
Feb 08, 2021 |
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) |
GSE138891 |
Cytotoxic CNS-associated T cells drive axon degeneration in aging and myelin disease |
|
Relations |
BioSample |
SAMN13032453 |
SRA |
SRX6996172 |