|
| Status |
Public on Jan 11, 2022 |
| Title |
Healthy Mouse Liver Nuclei_Mouse_002_Sample_001 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
shortfilename: ABU17
strain: C57Bl/6
platform: 10x Genomics – v3.1
digestion method: Nuclei
number of added abs: 0
number of cells: 2330
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches. Cell. 2022.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_002_Sample_001
|
| Data processing |
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq (version 3.1.0 or version 3.0.2)
Demultiplexed data was then processed using the Cell Ranger count pipeline (version 3.1.0 or version 3.0.2).
Cite-seq samples were mapped against the TotalSeqA whitelist.
Genome_build: mm10 (Mouse), hg19 (Human), GRCz10 (Zebrafish), MesAur1.0.100 (Hamster), GRCg6a.96 (Chicken), Sscrofa11.1.96 (Pig) or Macaca_facicularis_5.0.100 (Macaque)
Supplementary_files_format_and_content: h5 or txt files including raw gene – and if present – antibody counts (output CellRanger Count)
Supplementary_files_format_and_content: rds file: Seurat object
|
| |
|
| Submission date |
Dec 29, 2021 |
| Last update date |
Apr 06, 2024 |
| Contact name |
Liesbet Martens |
| E-mail(s) |
liesbet.martens@irc.vib-ugent.be
|
| Organization name |
VIB-University of Ghent
|
| Department |
VIB Inflammation Research Center
|
| Street address |
Technologiepark 927
|
| City |
Zwijnaarde |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE192740 |
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (single cells) |
| GSE192742 |
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches |
|
| Relations |
| BioSample |
SAMN24495538 |
| SRA |
SRX13549164 |
