|
Status |
Public on Nov 03, 2023 |
Title |
RN_brain_LPS |
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: LPS
|
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 |
SAMN36065301 |
SRA |
SRX20823725 |