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GSE20741
Mus musculus
12 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip
Description
Recently, we have shown that disturbed flow caused by partial ligation of mouse carotid artery rapidly induces endothelial dysfunction and atherosclerosis within two weeks. To understand the molecular mechanisms by which disturbed flow induces atherosclerosis, we carried out genome-wide microarray study using endothelial RNAs isolated from the flow-disturbed left and the contralateral right common carotid artery (LCA and RCA) in C57BL/6 mice.
Publication Title
Discovery of novel mechanosensitive genes in vivo using mouse carotid artery endothelium exposed to disturbed flow.
Sample Metadata Fields
Sex, Specimen part, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Microarray analysis was used to compare the gene expression profiles of Deaf-1-transduced mouse mammary epithelial cells (MECs) relative to Deaf-1-deficient MECs.
Publication Title
Deaf-1 regulates epithelial cell proliferation and side-branching in the mammary gland.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 19 Downloadable Samples
Illumina HiSeq 2000
Description
Purpose: The aim of this study is to determine the absolute and relative expression levels of mRNA transcripts across multiple flow cytometrically sorted epithelial cell types including freshly isolated CD24+CD29hi mammary stem cell-enriched basal cells (MaSC/basal), CD24+CD29loCD61+ luminal progenitor-enriched (LP) and the CD24+CD29loCD61- mature luminal-enriched (ML) cell populations. Additionally, a comparison between these primary cell types and cultured MaSC/Basal-derived mammosphere cells (mammosphere) and the CommaD-ßGeo (CommaDß) cell line was performed. Methods: Total RNA was extracted and purified from sorted luminal or basal populations from the mammary glands of female virgin 8- to 10-week-old FVB/N mice (3 independent samples per population), MaSC/Basal cells cultured for 1 week under mammosphere conditions and CommaDß cells grown under maintenance conditions (Deugnier et al. 2006). Total RNA (100 ng) was used to generate sequencing libraries for whole transcriptome analysis following Illumina’s TruSeq RNA v2 sample preparation protocol. Completed libraries were sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp single-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Approximately 30 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.14.1) (Liao et al. 2013). Single reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014). Overall design: Total RNA was extracted and purified from sorted luminal or basal populations from the mammary glands of female virgin 8- to 10-week-old FVB/N mice (3 independent samples for population), MaSC/Basal cells cultured for 1 week under mammsophere conditions and CommaDß cells grown under maintenance conditions (Deugnier et al. 2006) and their transcriptomes analysed by RNA-Seq.
Publication Title
A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 422 Downloadable Samples
- NextSeq 500
Description
Mammary glands were collected from 8 pubescent (4.7-4.9 week-old) female mice and 8 adult (10 week old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads. Overall design: RNA-seq profiling was completed for 221 cells from pubescent mice and 223 cells from adult mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 346 Downloadable Samples
- Illumina HiSeq 2000
Description
Mammary glands were collected from pre-pubescent (2 weeks old), pubescent (4.7- 4.9 weeks old) and adult (10 week-old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100 bp paired-end reads. Overall design: RNA-seq profiling was completed for 144 cells from 8 pre-puberty (2 week old) mice, 136 cells from 8 pubescent (4.7-4.9 week old) mice and 66 cells from 8 adult (10 week old) mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 311 Downloadable Samples
- NextSeq 500
Description
Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 adult (10 week old) female mice. Basal epithelial cells were FACS sorted. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads. Overall design: RNA-seq profiling was completed for 75 cells from pregnant mice and 237 cells from adult mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 278 Downloadable Samples
- NextSeq 500
Description
Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 non-pregnant adult (10 week old) female mice. Epithelial cells were FACS sorted from the pregnant mice. Cells from the adult mice were FACS sorted as basal or luminal. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve 75 bp paired-end reads. Overall design: 112 basal cells and 43 luminal cells were profiled from the adult mice. 123 total epithelial cells were profiled from the pregnant mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 169 Downloadable Samples
- Illumina HiSeq 2000
Description
Mammary glands of 8 adult (10 week-old) female mice were collected. Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100bp paired-end reads. Overall design: 96 basal and 90 luminal cells were profiled from 8 mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
T cell differentiation is governed by interactions with thymic epithelial cells (TECs) and defects in this process undermine immune function and tolerance. To uncover new strategies to restore thymic function and adaptive immunity in immunodeficiency, we sought to determine the molecular mechanisms that control life and death decisions in TEC. We created a mouse model which specifically deleted the pro-survival gene Mcl1 in TEC. We found that while BCL-2 and BCL-XL were dispensable for TEC homeostasis, MCL-1 deficiency impacted on TEC as early as E15.5, resulting in early thymic atrophy and T cell lymphopenia, with near complete loss of thymic tissue by 2 months of age. MCL-1 was not necessary for TEC differentiation but was continually required for the survival of medullary TEC, including autoimmune regulator (AIRE) expressing TECs and the maintenance of overall thymic architecture. To understand the molecular mechanisms in more detail, RNA-seq profiling was undertaken of cortical and medullary thymic epithelial cells (cTECs and mTECs) from wildtype and knockout mice. Overall design: The number of biological replicates was n=4 for WT cTECs, n=2 for WT mTECs, n=1 for KO cTECs and n=1 for KO mTECs.
Publication Title
A critical epithelial survival axis regulated by MCL-1 maintains thymic function in mice.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 2 Downloadable Samples
- NextSeq 500
Description
Epithelial cells were isolated by FACS from the mammary glands of adult (10 week old) female mice. A basal subpopulation of the epithelial cells was also isolated. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on an Illumina NextSeq500 sequencer to achieve 75 bp paired-end reads. Overall design: Transcriptional profiling was completed for 4771 basal cells and 3302 total epithelial cells from 8 mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples