|
| Status |
Public on Jan 20, 2021 |
| Title |
Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Reconstruction of heterogeneity through single-cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remain elusive in physical space. Here, we implement Spatial Transcriptomics to perform transcriptomic analysis across sectioned liver tissue. We confirm that the heterogeneity in this complex tissue is predominantly determined by lobular zonation. By introducing novel computational approaches, we enable transcriptional gradient measurements between tissue structures, including several lobules in a variety of orientations. Further, our data suggests the presence of previously transcriptionally uncharacterized structures within liver tissue, contributing to the overall spatial heterogeneity of the organ. This study demonstrates how comprehensive spatial transcriptomic technologies can be used to delineate extensive spatial gene expression patterns in the liver, indicating its future impact for studies of liver function, development and regeneration as well as its potential in pre-clinical and clinical pathology. Additional data to reproduce the data presented in this study with instrctions can be found at https://github.com/almaan/ST-mLiver and https://zenodo.org/record/4399655
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| |
|
| Overall design |
Spatial Transcriptomics analysis of 8 wildtype murine liver sections from 2 lobes
|
| |
|
| Contributor(s) |
Hildebrandt F, Ankarklev J |
| Citation(s) |
34857782 |
| |
| Submission date |
Jan 19, 2021 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Franziska Frederike Annalena Hildebrandt |
| E-mail(s) |
franziska.hildebrandt@su.se
|
| Phone |
+46702186657
|
| Organization name |
Stockholm University
|
| Department |
Department of Molecular Biosciences, the Wenner-Gren Institute
|
| Lab |
Group Ankarklev
|
| Street address |
Svante Arrhenius Väg 20c, MBW, Stockholms University
|
| City |
Stockholm |
| State/province |
Stockholms Lan |
| ZIP/Postal code |
10691 |
| Country |
Sweden |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA693336 |
| SRA |
SRP302449 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE165141_RAW.tar |
52.0 Mb |
(http)(custom) |
TAR (of TSV) |
| GSE165141_spot_ST_CN16_Liver_D1_0.1.tsv.gz |
16.1 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN16_Liver_D2_0.1.tsv.gz |
6.1 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN16_Liver_E1_0.1.tsv.gz |
17.2 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN16_Liver_E2_0.1.tsv.gz |
6.2 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN65_Liver_C1_0.1.tsv.gz |
8.1 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN65_Liver_C2_0.1.tsv.gz |
7.3 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN65_Liver_D1_0.1.tsv.gz |
8.1 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN65_Liver_D2_0.1.tsv.gz |
8.0 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN65_Liver_E1_0.1.tsv.gz |
7.5 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN73_Liver_C1_0.1.tsv.gz |
8.4 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN73_Liver_D1_0.1.tsv.gz |
8.6 Kb |
(ftp)(http) |
TSV |
| GSE165141_spot_ST_CN73_Liver_E2_0.1.tsv.gz |
8.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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