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Series GSE84498 Query DataSets for GSE84498
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
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.
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.
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
Submission date Jul 18, 2016
Last update date May 15, 2019
Contact name Keren Bahar-Halpern
Organization name Weizmann Institute
Lab Itzkovitz
Street address Herzl St 234
City Rehovot
ZIP/Postal code 7610001
Country Israel
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (26)
GSM2238401 AB911
GSM2238402 AB912
GSM2238403 AB913
BioProject PRJNA329488
SRA SRP078795

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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
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