Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Isoseq of VPA treated hepatocytes

ABSTRACT: Long Read Transcriptome Sequencing of primary human hepatocytes treated with VPA using PacBio Isoseq

PROVIDER: PRJEB46194 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR6221531.fastq.gz	Fastqsanger.gz
	ERR6221532.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Protein data in PHH after VPA-treatment

Project description:LC-MS/MS protein data of Primary Human Hepatocytes (PHH) exposed to Valproic Acid (VPA) for 3 days daily and 3 days daily exposure followed by 3 days washout.

2018-02-27 | PXD007538 | Pride

RNA-seq of Primary Human Hepatocytes (PHH) exposed to Valproic Acid (VPA) for 3 days daily and 3 days daily exposure followed by 3 days washout.

Project description:Primary Human Hepatocytes (PHH) were exposed daily for 3 days to 15 mM VPA after which RNA was isolated. After terminating the VPA treatment, part of the cells were kept with medium for 3 days in order to investigate the eventual persistence of VPA-induced methylome changes. Identification of differentially expressed regions in the RNA was carried out by the RNA-seq method.

2018-02-23 | E-MTAB-5984 | biostudies-arrayexpress

MeDIP profiling by high-throughput sequencing of Primary Human Hepatocytes (PHH) exposed to Valproic Acid (VPA) for 5 days daily and 5 days daily exposure followed by 3 days washout.

Project description:Primary Human Hepatocytes (PHH) were exposed daily for 5 days to 15 mM VPA after which DNA was isolated. After terminating the VPA treatment, part of the cells were kept with medium for 3 days in order to investigate the eventual persistence of VPA-induced methylome changes. Identification of methylated regions in the DNA was carried out by the Methylated DNA Immuno-Precipitation - sequencing (MeDIP-seq) method and contains the following steps: fragmentation, library preparation, MeDIP, and sequencing.

2017-09-25 | E-MTAB-4437 | biostudies-arrayexpress

MeDIP profiling by high-throughput sequencing of Primary Human Hepatocytes (PHH) exposed to Valproic Acid (VPA) for 3 days daily and 3 days daily exposure followed by 3 days washout.

Project description:Primary Human Hepatocytes (PHH) were exposed daily for 3 days to 15 mM VPA after which DNA was isolated. After terminating the VPA treatment, part of the cells were kept with medium for 3 days in order to investigate the eventual persistence of VPA-induced methylome changes. Identification of methylated regions in the DNA was carried out by the Methylated DNA Immuno-Precipitation - sequencing (MeDIP-seq) method and contains the following steps: fragmentation, library preparation, MeDIP, and sequencing.

2018-02-23 | E-MTAB-5983 | biostudies-arrayexpress

SHAPE:Isoseq

Project description:SHAPE:Isoseq

| PRJEB55218 | ENA

Black swan ISOseq Data

Project description:This study provide PacBio Isoseq RNA sequencing data for black swan (Cygnus_atratus) .

| PRJEB38871 | ENA

PacBio RNAseq(IsoSeq) for 1000 Genome Trio Samples

Project description:PacBio RNAseq(IsoSeq) for 1000 Genome Trio Samples

| PRJEB13749 | ENA

Expression data from untreated and valproic acid (VPA) treated CD34+ Hematopoietic Stem Cells (HSCs)

Project description:Histone deacetylase (HDAC) inhibitors are widely utilized in hematopoietic malignance therapy; nevertheless, little is currently known concerning their effects on normal myelopoiesis. In order to investigate a putative interference of HDAC inhibitors in myeloid commitment of hematopoietic stem/progenitor cells (HSPCs) we treated CD34+ cells with valproic acid (VPA). Moreover, we investigate changes in gene expression induced by VPA treatment on HSPCs, by means of microarray analysis in VPA treated and untreated (CTR) CD34+ cells. VPA treatment induced H4 histone acetylation in CD34+ cells and blocked them in G0-G1 phase of cell cycle. CD34 expression is maintained for a longer time in VPA treated cells, while the physiological decrease of CD34 antigen occurred in CTR cells. Moreover, VPA favored erythrocyte and megakaryocyte differentiation at the expense of granulocyte and mono-macrophage lineages, as demonstrated by immunophenotyping, morphological and clonogenic analysis. Finally, we demonstrated that VPA up-regulated master gene regulators of erythrocyte and megakaryocyte differentiation (GFI1B and MLLT3) through histone iper-acetylation of their promoters. These results indicate that VPA treatment enhances erythrocyte and megakaryocyte differentiation at the expense of granulocyte and mono-macrophage one. Microarray data provide for the first time a detailed molecular support for the biological effects promoted by VPA treatment in HSPCs.

2013-04-11 | GSE31283 | GEO

Gene expression of VPA and GEM

Project description:Background: Histone deacetylase (HDAC) is strongly associated with epigenetic regulation and carcinogenesis, and its inhibitors induce the differentiation or apoptosis of cancer cells. Valproic acid (VPA) is one of the clinically available HDAC inhibitors. We investigated the anticancer effects of VPA in combination with gemcitabine (GEM) in cholangiocarcinoma cell line, and explored the mechanisms of the anticancer effects using microarray analysis. Methods: A human cholangiocarcinoma cell line (HuCCT1) was used. The anticancer effects of VPA, or gemcitabine (GEM), and the effects of VPA combined with GEM, were studied by cell proliferation assay. The microarray analysis was performed, the genes were picked up using Gene Spring GX11.5, Ingenuity Pathways Analysis (IPA) was performed, and then the gene-expression was determined by RT-PCR. Results: GEM (5nM) and VPA (0.5mM) reduced by 23%, which significantly augmented the anticancer effect of GEM alone or VPA alone (P<0.01). Using the microarray analysis, forty-three genes were identified with the comparison between GEM group and GEM plus VPA combination group. The interactions were shown between genes of the “Cellular Development” relevant to the differentiation of cancer cell using IPA.

2011-02-09 | GSE27036 | GEO

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA

Project description:Valproic acid (VPA) is one of the most commonly used anti-epileptic drugs with pharmacological actions on GABA and blocking voltage-gated ion channels. VPA also inhibits histone deacetylase (HDAC) activity. Suberoylanilide hydroxamic acid is also a member of a larger class of compounds that inhibit HDACs. At the time of this article, there are 123 active international clinical trials for VPA (also known as valproate, convulex, divalproex, and depakote) and SAHA (vorinostat, zolinza). While it is well known that VPA and SAHA influence the accumulation of acetylated lysine residues on histones, their true epigenetic complexity remains poorly understood. Primary human cells were exposed to VPA and SAHA to understand the extent of histone acetylation (H3K9/14ac) using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Because histone acetylation is often associated with modification of lysine methylation, we also examined H3K4me3 and H3K9me3. To assess the influence of the HDAC inhibitors on gene expression, we used RNA sequencing (RNA-seq).

2024-09-04 | GSE276338 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data