|
| Status |
Public on Nov 03, 2023 |
| Title |
RN_brain_Saline |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: brain
genotype: WT
strain: Crl:CD(SD) (Charles River)
Sex: Female
age: 12 weeks old
treatment: Saline
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei extraction buffer (Miltenyi) and discontinuous iodixanol gradient separation were used to generate single nuclei suspensions, in accordance with manufacturers' protocols.
Libraries were prepared using Chromium Next GEM Single Cell 5´GEM, Library & Gel Bead Kit v5.2, Chromium Next GEM Chip K Single Cell Kit and Single Index Kit TT Set A (all 10x Genomics, Pleasanton, CA, USA), as per standard manufacturers' protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics Next GEM 5'v2 generated single nucleus cDNA library
|
| Data processing |
Raw sequencing data were demultiplexed, aligned to the rattus norvegicus reference genome mRatBN7.2 and counted using Cell Ranger (version 7.0.0; 10x Genomics).
Assembly: mRatBN7.2
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files contain filtered count gene UMI counts for each sample (=Filtered feature-barcode matrix). Files represent standard barcodes.tsv, features.tsv and matrix.mtx outputs from Cell Ranger (version 7.0.0; 10x Genomics).
|
| |
|
| Submission date |
Jun 29, 2023 |
| Last update date |
Nov 03, 2023 |
| Contact name |
Daniel Bormann |
| E-mail(s) |
daniel.bormann@meduniwien.ac.at
|
| Organization name |
Medical University of Vienna
|
| Department |
Department of Thoracic Surgery
|
| Lab |
Applied Immunology Laboratory
|
| Street address |
Waehringer Guertel 18-20
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE236114 |
Single nucleus gene expression profile of the rodent brains response to systemic innate immune system challenges |
|
| Relations |
| BioSample |
SAMN36065308 |
| SRA |
SRX20823724 |
