|
| Status |
Public on Jan 11, 2022 |
| Title |
Western diet fed (24 weeks) Liver CD45- cells_Mouse_003_Sample_001 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
shortfilename: CS124
strain: C57Bl/6
platform: 10x Genomics – v3
digestion method: In Vivo
number of added abs: 107
number of cells: 15065
|
| 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 HiSeq 4000 |
| |
|
| Description |
Total RNA
Liver_CD45- Cells_WD_24wks_Mouse
Western diet fed (24 weeks) Liver CD45- cells_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.
|
| 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 |
GPL21103 |
| 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 |
SAMN24495480 |
| SRA |
SRX13549235 |
