|
| Status |
Public on Jan 11, 2022 |
| Title |
Standard diet fed (36 weeks) Mouse Liver_Mouse_001_Sample_001 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
shortfilename: JBO006
strain: C57Bl/6
platform: 10x Visium
condition: SD
number of added abs: 0
number of spots: 1279
|
| 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 |
Whole Liver_SD_36Wks_Visium_Mouse
Standard diet fed (36 weeks) Mouse Liver_Mouse_001_Sample_001
|
| Data processing |
Raw sequencing data for each sample was converted to matrices of expression counts using the Space Ranger software provided by 10X Genomics (version 1.0).
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: h5 file including raw gene count (output Space Ranger) or txt file including raw antibody counts
Supplementary_files_format_and_content: json file including scale factors (output Space Ranger)
Supplementary_files_format_and_content: png file including tissue image (output Space Ranger)
Supplementary_files_format_and_content: csv file including tissue positions (output Space Ranger)
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) |
| GSE192741 |
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial) |
| GSE192742 |
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches |
|
| Relations |
| BioSample |
SAMN24495435 |
| SRA |
SRX13549298 |
