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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 06, 2018 |
| Title |
Transcriptional and Epigenomic Landscapes of CNS and non-CNS Vascular Endothelial Cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Vascular endothelial cell (EC) function depends on appropriate organ-specific molecular and cellular specializations. To explore genomic mechanisms that control this specialization, we have analyzed and compared the transcriptome, accessible chromatin, and DNA methylome landscapes from mouse brain, liver, lung, and kidney ECs. Analysis of transcription factor (TF) motifs at candidate cis-regulatory elements together with TF gene expression reveals both shared and organ-specific EC TFs. In the embryo, only those ECs that are adjacent to or within the developing CNS exhibit canonical Wnt signaling, which correlates precisely with blood-brain barrier (BBB) differentiation and Zic3 expression. In acutely cultured brain ECs, the rapid loss of BBB markers is closely correlated with down-regulation of canonical Wnt signaling. In the early postnatal brain, single cell RNA-seq of purified ECs reveals close relationships between veins and mitotic cells and between arteries and tip cells, and a division of capillary ECs into vein-like and artery-like classes.
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| Overall design |
RNA-seq and MethylC-seq of postnatal day 7 (P7) vascular endothelial cells (ECs) from brain, liver, lung, and kidney of Tie2-GFP mice; RNA-seq and ATAC-seq of primary brain EC culture; single cell RNA-seq of P7 mouse brain ECs
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| Contributor(s) |
Sabbagh MF, Heng J, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J |
| Citation(s) |
30188322, 31913116 |
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| Submission date |
Mar 14, 2018 |
| Last update date |
Jan 13, 2020 |
| Contact name |
Mark F Sabbagh |
| E-mail(s) |
msabbag2@jhmi.edu
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| Organization name |
Johns Hopkins University School of Medicine
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| Department |
Molecular Biology and Genetics
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| Lab |
Jeremy Nathans
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| Street address |
725 North Wolfe Street
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (42)
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| Relations |
| BioProject |
PRJNA438341 |
| SRA |
SRP135700 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE111839_ATAC-seq.bed.tar.gz |
550.0 Kb |
(ftp)(http) |
TAR |
| GSE111839_MethylC-seq.bed.tar.gz |
3.8 Mb |
(ftp)(http) |
TAR |
| GSE111839_RAW.tar |
36.7 Gb |
(http)(custom) |
TAR (of BW, MTX, NARROWPEAK, TAR, TSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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