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Series GSE144839 Query DataSets for GSE144839
Status Public on Jan 04, 2021
Title Cardiac endothelial cells maintain open chromatin and expression of cardiomyocyte myofibrillar genes
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Endothelial cells (ECs) are widely heterogenous depending on tissue and vascular localization. Jambusaria et al. recently demonstrated that ECs in various tissues surprisingly possess mRNA signatures of their underlying parenchyma. The mechanism underlying this observation remains unexplained, and could include mRNA contamination during cell isolation, in vivo mRNA paracrine transfer from parenchymal cells to ECs, or cell-autonomous expression of these mRNAs in ECs. Here, we use a combination of bulk RNASeq, single-cell RNASeq datasets, in situ mRNA hybridization, and most importantly ATAC-Seq of FACS-isolated nuclei, to show that cardiac ECs actively express cardiomyocyte myofibril (CMF) genes and have open chromatin at CMF gene promoters. These open chromatin sites are enriched for sites targeted by cardiac transcription factors, and closed upon expansion of ECs in culture. Together, these data demonstrate unambiguously that the expression of CMF genes in ECs is cell-autonomous, and not simply a result of technical contamination or paracrine transfers of mRNAs, and indicate that local cues in the heart in vivo unexpectedly maintain fully open chromatin in ECs at genes previously thought limited to cardiomyocytes.
Overall design NuTRAP/Cdh5-Cre (NuTRAP from Roh, 2017, Cell Reports) animals were generated to GFP tag endothelial cell nuclei. Total nuclei were isolated from whole hearts of 8-12week old male animals. Endothelial cell nuclei (GFP+) were isolated by flow cytometry in addition to non-endothelial nuclei (GFP-).
100-50,000 purified GFP+ ("Pos") and GFP- ("Neg") nuclei were processed for ATACSeq, using the protocol outlined in Buenrostro, et al 2013, using 2.5uL of Tn5 per 50,000 nuclei.

Please note that *narrowPeak data was generated from both replicates and is linked to the corresponding *1_ATACSeq sample records.
Contributor(s) Yucel ND, Arany Z
Citation(s) 33315013
Submission date Feb 06, 2020
Last update date Jan 06, 2021
Contact name Arndt Siekmann
Department Perelman School of Medicine
Lab Arndt Siekmann
Street address 421 Curie Boulevard, 1114 Biomedical Research Building II/III
State/province Pennsylvania
ZIP/Postal code 19103
Country USA
Platforms (2)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (4)
GSM4299073 HeartNeg1_ATACSeq
GSM4299074 HeartPos1_ATACSeq
GSM4299075 HeartNeg2_ATACSeq
BioProject PRJNA605116
SRA SRP247492

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE144839_RAW.tar 827.1 Mb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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