Project description:We reported loss of HBL1 lnRNA promoted cardiogenesis and the interaction of HBL1-EED in hiPSCs. Here we used specific EED and H3K27me3 antibodies to pull down their binding genomic DNAs in hiPSCs, respectively, which let us know the potential genes regulated by HBL1-EED-H3K27me3 during cardiogenesis. 1% Input samples were collected from the same samples after chromatin shearing.
Project description:We reported loss of ARID1A promoted neurogenesis and inhibited cardiogenesis. Under microscopy, we observed that spontaneously differentiated cells were induced in ARID1A KO H9 hESCs cultured in mTesR medium. We did not know what cells types were. Here ATAC-seq were used to investigate chromatin accessibilities change in differentiated (day 4) WT H9 hESCs and ARID1A KO hESC cells.
Project description:Compare difference Global expression profile of hiPSCs between hESCs and human Somatic cells, showing that hiPSCs and hESCs is consistent in lineages and indicated that the induce method is safe and reliable. There are three groups of samples, each group has two repeated samples, hiPSCs respectively compared with hESCs and human Urine-Derived Cells.
Project description:Compare difference Global expression profile of hiPSCs between hESCs and human Somatic cells, showing that hiPSCs and hESCs is consistent in lineages and indicated that the induce method is safe and reliable.
Project description:In our study, PRDM14 and NFRkB were found to enhance the reprogramming of human fibroblasts to hiPSCs in the presence of OCT4, SOX2, KLF4, with/without c-MYC (OSK/OSKC). To examnie if the obtained hiPSC share similar expression signature with hESC, we conducted the microarray analysis on the hiPSCs, hESCs and fibroblasts. The result showed that all of the examined hiPSCs resembled hESCs, but differed from fibroblasts MRC5. 4 hiPSC lines, 2 hESC lines and 1 type of fibroblasts were analyzed in total. Each sample is done in duplicates.
Project description:Despite significant progresses, the genetic roles of regulatory elements in gene expression still remain largely unknown in prostate cells. Recent development in single cell sequencing has made it possible to combine ATAC-seq and RNA-seq to determine genome-wide linkages between chromatin accessibilities and gene expression. To test the feasibility of using single cell multiome sequencing in dissecting regulatory linkages between chromatin accessibilities and gene expressions, we applied 10X Multiome ATAC + Gene Expression platform to simultaneously encapsulate Tn5 transposase tagged nuclei from multiple prostate cell lines. Based on these multiomic data, we developed subsampling linkage analysis to identify linkage associations between open chromatin and gene expressions. Moreover, we implemented an innovative analytical method to investigate RNA expression alterations related to germline variant locus accessibilities at single cell levels, i.e., expression quantitate accessible loci (eQAL) analysis. Our data and methodology will complement traditional eQTL analysis and foresee more genetic applications aiming to clarify regulatory elements by single cell sequencing.
Project description:To determine the role of estrogen-related receptor alpha and gamma (ERRa/g) on chromatin accessibility, we performed ATAC-seq studies with WT control and ERRa/g KO hiPSC-CMs. We found that ERRa/g activates cardiac chromatin accessibilities in hiPSC-CMs. A subset of the decreased ATAC signals by loss of ERRa/g overlapped ERRg peaks (GSE113760) in hiPSC-CMs, suggesting that ERRg might be directly involved in the activation of cardiac chromatin accessibilities. The motif analysis with decreased ATAC signal by loss of ERRa/g revealed that cardiac-enriched transcription factors such as MEF2 and GATA could cooperate with ERR.
Project description:In our study, PRDM14 and NFRkB were found to enhance the reprogramming of human fibroblasts to hiPSCs in the presence of OCT4, SOX2, KLF4, with/without c-MYC (OSK/OSKC). To examnie if the obtained hiPSC share similar expression signature with hESC, we conducted the microarray analysis on the hiPSCs, hESCs and fibroblasts. The result showed that all of the examined hiPSCs resembled hESCs, but differed from fibroblasts MRC5.
