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Series GSE111930 Query DataSets for GSE111930
Status Public on Aug 11, 2020
Title An endogenous retrovirus-derived long non-coding RNA promotes fetal cardiomyocyte migration in primates
Organisms Macaca mulatta; Gorilla gorilla; Pan troglodytes; Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The protein-coding gene networks regulating heart development are well known. Less understood are the roles of long non-coding RNAs (lncRNAs), many of which are poorly conserved due to their origins from transposable elements (TEs) such as endogenous retroviruses (ERVs). Here, we report hundreds of ERV elements from the primate-specific MER41 family are expressed in pluripotent cell-derived cardiomyocytes and fetal heart, some of which are regulated by the cardiogenic transcription factor TBX5. The most significant of these are located within BANCR, an lncRNA exclusively expressed in primate fetal cardiomyocytes in normal physiology. Surprisingly, BANCR promotes cellular movement in fetal cardiomyocytes, which is due in part to Rho GTPase and ephrin receptor signaling. We postulate that ERV-derived BANCR is a recent evolutionary mechanism for enabling larger heart sizes in primates, and underscores the remarkable retroviral origins of humans.
Overall design We performed RNA-seq of human fetal tissues, and iPSCs and cardiomyocytes derived from iPSCs (iPSC-CMs) in both human and non-human primate cell lines (chimpanzee, gorilla, rhesus macaque).
We also performed both RNA- and ATAC-seq of hESC-CMs with constitutive BANCR shRNA knockdown (BKD), lentiviral constitutive over-expression (BOE), as well as H3K27ac HiChIP in human iPSC-CMs. RNA-seq was also performed on E16 transgenic mouse embryo hearts with human BANCR expression, and compared with littermate control hearts.
YAP1 ChIP-seq was performed with anti-YAP1 antibody (Novus; NB110).
Contributor(s) Wilson KD, Ameen M, Tian L, Zhang Y, Mumbach M, Guo H, Wu JC
Citation(s) 32763147
Submission date Mar 16, 2018
Last update date Aug 13, 2020
Contact name Lei Tian
Phone 6502388262
Organization name Stanford's Postdoctoral Scholar programs
Street address 1215 Welch Rd
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (7)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (60)
GSM3045196 ciPSC
GSM3045197 ciPSC-CM
GSM3045198 giPSC
BioProject PRJNA438592
SRA SRP135857

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 466.5 Kb (ftp)(http) TXT
GSE111930_MBOE_read_counts.txt.gz 192.7 Kb (ftp)(http) TXT
GSE111930_RAW.tar 17.1 Gb (http)(custom) TAR (of BW, HIC, TDF, TXT)
GSE111930_WT_hPSC-CM_HiChIP_H3K27ac_combined.hic 927.0 Mb (ftp)(http) HIC
GSE111930_WT_hPSC-CM_HiChIP_H3K27ac_combined_FitHiCq7_5kb_WashU.txt.gz 896.3 Kb (ftp)(http) TXT
GSE111930_fetal_tissues_read_counts.txt.gz 909.6 Kb (ftp)(http) TXT 634.1 Kb (ftp)(http) TXT
GSE111930_raw_counts.txt.gz 602.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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