|
| Status |
Public on Oct 23, 2023 |
| Title |
DA1-snRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
cell dissociation: Total Liver Homogenate (CST nuclei extraction)
strain: Dark Agouti
Sex: M
disease state: healthy
assay: 10x Genomics Single Cell 3’ v3
|
| Growth protocol |
The animals were co-housed in the Animal Research Center facility at Princess Margaret Research Tower and were fed a standard diet of sterilized water and laboratory blocks.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were prepared as outlined by the 10x Genomics Single Cell 3’ v2 (scRNA-seq TLH samples) and v3 (immune-enriched samples and snRNA-seq samples) Reagent Kit user guides and as described previously (Andrews et al., 2022; MacParland et al., 2018). Briefly, following cell counting (using Trypan blue exclusion for single cell and SYBR green II for single nuclei), we targeted the capture of 9000 cells and loaded them onto the 10x Genomics Single cell A Chips for the total liver homogenate,and B Chips for the immune-enriched and snRNA-seq samples. Visium spatial transcriptomics were sequined at 60,000 reads per spot with 2400 and 2500 number of spots for sample A1 and B1, respectively. cDNA libraries were prepared as per the Single Cell 3′ Reagent Kits v3 user guide and Visium Spatial Gene Expression Reagent Kits user guide for spatial transcriptomics. scRNA-seq TLH were sequenced on a HiSeq 2500. Visium spatial transcriptomics, snRNA-seq and immune-enriched samples were sequenced on a NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger 3.1.0, and 10x Genomics Space Ranger 1.1.0 pipelines
Assembly: Rattus_norvegicus.custom_6.0.98-
Supplementary files format and content: Matrix files (.mtx)
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Delaram Pouyabahar |
| E-mail(s) |
d.pouyabahar@mail.utoronto.ca
|
| Phone |
+1(647)6743771
|
| Organization name |
University of Toronto
|
| Department |
Molecular Genetics
|
| Lab |
Bader Lab
|
| Street address |
160 College St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5S 3E1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE220075 |
A Rat Liver Cell Atlas Reveals Intrahepatic Myeloid Heterogeneity. |
|
| Relations |
| BioSample |
SAMN36923776 |
| SRA |
SRX21325312 |
