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| Status |
Public on Nov 29, 2016 |
| Title |
Single-cell spatial reconstruction reveals global division of labor in the mammalian liver |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The mammalian liver consists of hexagonal-shaped lobules, radially polarized by blood flow and morphogens. Key liver genes have been shown to be differentially expressed along the lobule axis, a phenomenon termed zonation, but a detailed genome-wide reconstruction of this spatial division of labor has not been achieved. Here we measure the whole transcriptome of thousands of single mouse liver cells and infer their lobule coordinates using a panel of zonated landmark genes, characterized with single-molecule FISH. We obtain a genome-wide reconstruction of liver zonation profiles with unprecedented spatial resolution. We find that more than 50% of liver genes are significantly zonated and uncover abundant non-monotonic profiles that peak at the mid-lobule layers. Our approach can facilitate reconstruction of similar spatial genomic blueprints for other mammalian organs.
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| Overall design |
mRNA profiles from single cells extracted from mouse liver were generated by deep sequencing of 1736 of single cells, sequenced in several batches in an Illumina NextSeq.
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| Contributor(s) |
Itzkovitz S, Amit I, Bahar Halpern K, Matcovitch O, Shenhav R, Toth B, Lemze D, Landen S, Giladi A, Golan M, Baydatch S, Stokar Avihail A, David E, Brandis A, Massasa EE, Moor AE |
| Citation(s) |
28166538 |
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| Submission date |
Jul 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Keren Bahar-Halpern |
| Organization name |
Weizmann Institute
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| Lab |
Itzkovitz
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| Street address |
Herzl St 234
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA329488 |
| SRA |
SRP078795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84498_experimental_design.txt.gz |
14.6 Kb |
(ftp)(http) |
TXT |
| GSE84498_umitab.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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