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RNA-seq analysis of gene expression patterns responding to TSA treatment during hESC neural differentiation

ABSTRACT: We report the differential roles of an HDAC inhibitor-TSA during hESC nerual commitment. In the initiation of hESC differentiation, TSA could inhibit the downregulation of pluripotency genes to maintain pluripotency, whereas in the neural commitment stage, TSA could promote neural gene expression to assist hESC nerual determination.

ORGANISM(S): Homo sapiens

PROVIDER: GSE66777 | GEO | 2015/03/11

SECONDARY ACCESSION(S): PRJNA277945

REPOSITORIES: GEO

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RNA-seq analysis of gene expression patterns responding to TSA treatment during hESC neural differentiation

Project description:We report the differential roles of an HDAC inhibitor-TSA during hESC nerual commitment. In the initiation of hESC differentiation, TSA could inhibit the downregulation of pluripotency genes to maintain pluripotency, whereas in the neural commitment stage, TSA could promote neural gene expression to assist hESC nerual determination. Examination of gene expression patterns in hESCs, day 4 or day 8 differentiated cells without or with TSA treatment

2015-03-11 | E-GEOD-66777 | biostudies-arrayexpress

Gene expression after TSA treatment in H69 cells

Project description:Objective of the study is to determine global changes in gene expression after HDAC inhibitor Trichostatin (TSA) treatment in H69 cell line

2021-05-26 | GSE161313 | GEO

7.5uM CG-1521 and 5uM TSA treatment of LNCaP Prostate Cancer cells

Project description:Genome wide expression changes following treatment with the HDACs (Histone Deacetylase Inhibitor) CG-1521 (7.5uM) or TSA (Trichostatin A) were investigated to determine regulatory targets and patterns of the HDAC Inhibitors. Keywords: Expression response to treatment, data was used for a comparison of gene expression and regulation between CG-1521 and TSA in LNCaP Cells

2007-09-15 | GSE8645 | GEO

5Aza and TSA treatment of MCF7 cells (RNA-seq)

Project description:The goal of this study is to identify the gene expression changes caused by exposure of to the DNMT inhibitor 5-aza-2'-deoxycytidine (5Aza) and HDAC inhibitor Trichostatin A (TSA). We performed rRNA-depleted RNA sequencing of the untreated and drug-treated MCF7 breast cancer cell lines and carried out differential gene expression analysis. Although 5Aza caused a stranger demethylation effect than TSA, there were fewer differentially expressed gene in the 5Aza-treated MCF7 than the TSA-treated cells.

2016-06-30 | E-MTAB-3794 | biostudies-arrayexpress

Gene expression analysis of mouse testis after treatment with histone deacetylase inhibitor TSA

Project description:Trichostatin A (TSA) is one of the most potent reversible histone deacetylase (HDAC) inhibitors. In male mice, subcutaneous application of TSA is followed by infertility due to apoptosis of pachytene spermatocytes. To get more insight into the mechanisms underlying this phenomenon, we performed a genome-wide expression analysis of murine testes after TSA treatment. The whole genome transcriptome analysis revealed 507 significantly regulated genes. Validation by real-time quantitative PCR confirmed the expression of 7 from 9 genes tested (78%). Keywords: time course

2007-08-02 | GSE5448 | GEO

Effect of HDAC inhibitor TSA on haploid embryogenesis [dataset 1]

Project description:Haploid embryos can be induced from cultured immature pollen following a stress treatment. In Brassica napus, application of the histone/lysine deacetylase (HDAC/KDAC) inhibitor trichostatin A (TSA) to pollen cultures enhances the production of differentiated embryos and embryogenic callus when applied together with heat stress (Li et al., 2014). To identify genes associated with the induction of B. napus haploid embryogenesis, we compared the transcriptomes of untreated pollen cultures and pollen cultures treated with either heat-stress or heat-stress plus TSA.

2020-08-03 | GSE140969 | GEO

5Aza and TSA treatment of MCF7 cells (BS-seq)

Project description:The goal of this study is to identify the DNA methylation changes caused by exposure of to the DNMT inhibitor 5-aza-2â-deoxycytidine (5Aza) and HDAC inhibitor Trichostatin A (TSA). We performed whole-genome bisulfite sequencing of the drug-treated MCF7 breast cancer cell lines and compare their DNA methylation profile with the untreated MCF7 (see E-MTAB-2014). While MCF7 treated with both drugs experienced global loss of DNA methylation, the 5Aza induced stronger demethylation than TSA.

2016-06-30 | E-MTAB-3785 | biostudies-arrayexpress

HDAC6 regulates NF-κB signalling by HDAC-dependent and independent mechanisms to control chondrocyte IL-1-induced MMP and inflammatory gene expression [TSA exp]

Project description:Analysis of the effect of HDAC inhibitor TSA on IL-1-induced gene expression in SW1353 chondrocytes.

2021-10-29 | GSE186689 | GEO

Expression data from undifferentiated human embryonic stem cells (hESC) and Day 3.5 mesodermal progenitor (CD326neg CD56+) population

Project description:Our understanding of how mesodermal tissue is formed, has been limited by the absence of specific and reliable markers of early mesoderm commitment. We report that mesoderm commitment from human embryonic stem cells (hESC) is initiated by Epithelial to Mesenchymal transition (EMT) as shown by gene expression profiling and by reciprocal changes in expression of the cell surface proteins, EpCAM/CD326 and NCAM/CD56. Molecular and functional assays reveal that CD326negCD56+ cells, generated from hESC in the presence of activin A, BMP4, VEGF and FGF2, represent a novel, multi-potent mesoderm-committed progenitor population. CD326negCD56+ progenitors are unique in their ability to generate all mesodermal lineages including hematopoietic, endothelial, mesenchymal (bone, cartilage, fat, fibroblast), smooth muscle and cardiomyocytes, while lacking the pluripotency of hESC. CD326negCD56+ cells are the precursors of previously reported, more lineage-restricted mesodermal progenitors. These findings present a novel approach to study how germ layer specification is regulated, and offer a unique target for tissue engineering. We used microarrays to compare gene expression profile of early mesodermal progenitors with undifferentiated hESC (H9 line). Mesoderm induction from hESC was initiatiated with combination of morphogens and growth factors including activin A, bone morphogenic protein 4, basic fibroblast growth factor and vascular endothelial growth factor. Proposed mesodermal progenitor population was isolated by FACS on day 3.5 of culture based on the presence of CD56 expression and the absenbce of CD326 expression.

2010-05-27 | E-GEOD-21668 | biostudies-arrayexpress

Transcriptome analysis reveals determinant stages controlling human embryonic stem cell commitment to neuronal cells

Project description:Proper neural commitment is essential for ensuring the appropriate development of the human brain and for preventing neurodevelopmental diseases such as autism spectrum disorders, schizophrenia, and intellectual disorders. However, the molecular mechanisms underlying the neural commitment in humans remain elusive. Here, we report the establishment of a neural differentiation system based on human embryonic stem cells (hESCs) and on comprehensive RNA-Seq analysis of transcriptome dynamics during early hESC differentiation. Using weighted gene co-expression network analysis, we reveal that the hESC neurodevelopmental trajectory has five stages: pluripotency (day 0), differentiation initiation (days 2, 4, and 6), neural commitment (days 8–10), neural progenitor cell proliferation (days 12, 14, and 16), and neuronal differentiation (days 18, 20, and 22). These stages were characterized by unique module genes, which may recapitulate the early human cortical development. Moreover, a comparison of our RNA-Seq data with several other transcriptome profiling datasets from mice and humans indicated that module 3 associated with the day 8–10 stage is a critical window of fate switch from the pluripotency to the neural lineage. Interestingly, at this stage, no key extrinsic signals were activated. In contrast, using CRISPR-Cas9–mediated gene knockouts, we also found that intrinsic hub transcription factors, including the schizophrenia-associated SIX3 gene and septo-optic dysplasia–related HESX1 gene, are required to program hESC neural determination. Our results improve the understanding of the mechanism of neural commitment in the human brain and may help elucidate the etiology of human mental disorders and advance therapies for managing these conditions.

2017-10-18 | GSE103715 | GEO

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