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Identification of a hepatocyte stem cell and its niche in liver homeostasis

ABSTRACT: Summary: RNAseq analysis of Axin2+ hepatocyte stem cells versus Axin2- mature hepatocytes shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- hepatocytes. Methods: Hepatocytes were isolated from 8 week old Axin2rtTA;TetO-H2B-GFP mice (n = 3) given doxycycline in drinking water for 7 days. After removal of non-parenchymal cells, the hepatocytes were sorted into GFP+ versus GFP- populations by FACS. mRNA was isolated and RNAseq profiles were generated using Illumina HiSeq 2000. The reads were mapped to the mouse genome (mm10) using TopHat (v2.0.11) and differential gene expression analysis was performed using CuffDiff (v.2.2.2). Results: We mapped about 60 million sequence reads per sample to the mouse genome (build mm10) and identified more than 30,000 transcripts in the Axin2+ and Axin2- cell populations. Differential gene expression analysis using CuffDiff identified 96 genes with signficantly different expression levels between the two populations. Several of these were confirmed by RNA in situ and qRT-PCR analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE68806 | GEO | 2015/08/07

SECONDARY ACCESSION(S): PRJNA283831

REPOSITORIES: GEO

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Identification of a hepatocyte stem cell and its niche in liver homeostasis

Project description:Summary: RNAseq analysis of Axin2+ hepatocyte stem cells versus Axin2- mature hepatocytes shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- hepatocytes. Methods: Hepatocytes were isolated from 8 week old Axin2rtTA;TetO-H2B-GFP mice (n = 3) given doxycycline in drinking water for 7 days. After removal of non-parenchymal cells, the hepatocytes were sorted into GFP+ versus GFP- populations by FACS. mRNA was isolated and RNAseq profiles were generated using Illumina HiSeq 2000. The reads were mapped to the mouse genome (mm10) using TopHat (v2.0.11) and differential gene expression analysis was performed using CuffDiff (v.2.2.2). Results: We mapped about 60 million sequence reads per sample to the mouse genome (build mm10) and identified more than 30,000 transcripts in the Axin2+ and Axin2- cell populations. Differential gene expression analysis using CuffDiff identified 96 genes with signficantly different expression levels between the two populations. Several of these were confirmed by RNA in situ and qRT-PCR analysis. mRNA profiles of Axin2+ and Axin2- cells from uninjured adult mouse liver were analysed by deep sequencing, in triplicate, using Illumina HiSeq 2000.

2015-08-07 | E-GEOD-68806 | biostudies-arrayexpress

Endometrial Axin2+ cells drive epithelial homeostasis and regeneration, and develop endometrial cancer following oncogenic transformation

Project description:Summary: RNAseq analysis of Axin2+ and Axin2- endometrial epithelial cells shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- cells. Methods: Four-week-old Axin2rtTA; tetOH2BJGFP mice (n=3) were ovariectomized. After 2 weeks of rest, H2BJGFP was induced in Axin2+ cells by a single dose of doxycycline administered intraperitoneally and uteri were collected 4 days post-doxycycline administration. Endometrial epithelial cells were isolated, digested into single cell suspension and Axin2+ (GFPhigh) and Axin2- (GFP-) cells were FACS sorted. The respective Axin2+ and Axin2- cells from each of the three mice used in this experiment were pooled together (Axin2- cells = C1, C2, C3; Axin2+ cells = M1, M2, M3, Arabic numeral represents the mouse number). Total RNA was isolated using RNeasy Micro kit (Qiagen) as per manufacturer instructions. RNA quality and concentration were determined using Nanodrop ND-1000 Spectrophotometer. RNAseq profiles were generated using Illumina NovaSeq platform. The reads were mapped to the mouse genome (Build version mm10) using the STAR aligner (v2.5.3a) and differential gene expression analysis was performed using edgeR (version 3.22.5) tool. Results: Differential gene expression analysis using edgeR identified 4458 genes that were differentially expressed by more than twofold in the Axin2high population compared with Axin2- population. Several of these differentially expressed genes include some of the well-known stem cell markers.

2020-01-14 | GSE140222 | GEO

Expression data from mouse calvarial suture mesenchymal cells

Project description:Axin2-expressing calvarial suture stem cells can contribute to calvarial development, homeostatic maintenance, repair, and regeneration. We used microarray to examine the gene expression profiles of Axin2-expressing suture stem cells and Axin2-negative cells in suture mesenchyme. Three of Axin2+/GFP+ and three of Axin2-/GFP- cell samples were collected from mice carrying Axin2rtTA and TREH2BGFP transgenes. Each samples were isolated from 6-8 Axin2rtTA; TRE-H2BGFP mice and sorted by the GFP intensity.

2015-11-11 | E-GEOD-74849 | biostudies-arrayexpress

Project description:ATACseq of AXIN2-/+ hepatocytes and AXIN2+ intestinal stem cells (ISCs) and LGR4/5KO hepatocytes

| PRJNA716814 | ENA

Quantitative Analysis of Neurog2 Heterozygote, Mutant and and Mash1KI Retinal Transcriptomes by RNA Sequencing

Project description:To generate an unbiased view of changes to the retinal gene network in Neurog2 retinal mutants as well as understanding the effects of Mash1 ectopic expression in a Neurog2 retinal mutant, we generated and compared the E12.5 transcriptomes from Neurog2 heterozygote, Neurog2 mutant and Neurog2 mutant;Mash1 knock-in mice. A pair of E12.5 retinas from each biologic replicate underwent FACS sorting to isolate GFP+ cells. GFP+ cells were used to produce libraries for high throughput sequencing (n = 3 biologic replicates/genotype). Reads were aligned with BWA and Bowtie programs to the mm10 genome. Aligned reads were then analyzed for differentially expressed transcripts using the CuffDiff program in the Galaxy online bioinformatics package (www.usegalaxy.org).

2018-08-30 | GSE111666 | GEO

mRNA profiling of Asns-silenced murine 4T1-T breast cancer cells grown in the presence and absence of Asparagine

Project description:Murine 4T1-T breast cancer cells were infected with an shRNA targeting Asparagine Synthetase (Asns) and grown in DMEM +/- asparagine. Cells were harvested and processed with the NuGen Ovation RNAseq system V2. Libraries were sequenced on an Illumina platform and mapped using Bowtie2 to the mm10 genome prior to transcript quantification using HT-Count.

2018-02-07 | GSE104964 | GEO

mRNA Profiling of Murine 4T1 Breast Cancer Cells with Asns knocked down

Project description:Murine 4T1-T Breast cancer cells were infected with retroviral vectors harboring shRNAs for murine or a Renilla, as negative control. After selection cells were harvested and processed with the NuGen Ovation RNAseq system V2. Libraries were sequenced on an Illumina platform and mapped using Bowtie2 to the mm10 genome prior to transcript quantification using HT-Count.

2018-02-07 | GSE104967 | GEO

Delineating Tumor-infiltrating Antigen Presenting Cell populations

Project description:The goal of this study is to compare tumor-infiltrating antigen presenting cell populations by global transcriptome profiling (RNA-seq) to help further delineate sub-populations of infiltrating myeloid cells in tumor. Methods: Four tumor antigen presenting cell populations were sorted from digested B78chOVA (melanoma variant) tumors in biological triplicate Results: RNA was extracted from the 4 groups (n=3 per group) and prepared for RNAseq. Sequencing yielded ~405 million reads with an average read depth of 33.7 million reads/sample. Reads were then aligned to the mouse genome (UCSC mm10) and those that mapped uniquely to known mRNAs were used to assess differential expression.

2014-11-10 | GSE61462 | GEO

RNA-seq profiling of transcriptomes of control and Hif1a mutant E12.5 hearts

Project description:Purpose: to identify genes aberrantly expressed upon myocardial ablation of Hif1a Methods: a floxed Hif1a allele was deleted in mouse embryonic hearts using a NXK2.5Cre line. Total RNA was extracted from E12.5 hearts (n=3 for controls and mutants) usinz Trizol and processed for RNA-seq. Reads were mapped to Mm10 reference genome using TopHat2 and Bowtie2. Transcript expression values were determined after transcript normalization with AltAnalyze Results: this analysis revealed a total of 1451 genes significantely (|Fold| > 20% and P<0.05) modulated in Hif1a cKO hearts 6 total RNAseq runs with 3 experimental samples and 3 controls samples

2015-04-29 | E-GEOD-61209 | biostudies-arrayexpress

Tissue neutrophil heterogeneity

Project description:Purpose: The goals of this study are to compare bulk RNAseq profiles of tissue neutrophils. Methods: Bulk RNAseq of sorted neutrophils from bone marrow, spleen, blood, lung, peripheral blood, skin and intestine from wild-type (WT) mice, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with RSEM which mapped about 26 million sequence reads per sample to the mouse genome (build mm10/GRCm38) and identified 32328 genes.

2020-09-08 | GSE141745 | GEO

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