Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic characterization of cattle primary hepatocytes and its comparison with Madin-Darby bovine kidney (MDBK) cells and liver tissue

ABSTRACT: Cattle primary cultured hepatocytes (CHs) have been used as a useful in vitro model for drug metabolism studies. However, they suffer some limitations, when compared with the ex vivo liver tissue, such as difficult adhesion to the substrate following isolation, a limited viability and a rapid loss of differentiated characteristics. Therefore, a reliable hepatic in vitro model is actually needed for cattle. As established bovine hepatic cell lines are not available, we characterized the cattle primary CHs' transcriptome by using a cDNA microarray approach and compared it with ex vivo cattle liver tissue as well as with the Madin-Darby Bovine Kidney (MDBK) cells (as an established cell line for transfection purposes).
This part of the study compares the primary CHs vs. liver tissue. The comparison of MDBK cells vs. the primary CHs is found under E-MTAB-4430.

INSTRUMENT(S): Agilent G2565BA scanner, Agilent Hybridization Oven

ORGANISM(S): Bos taurus

SUBMITTER: Ramy Elgendy

PROVIDER: E-MTAB-4424 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic characterization of the Madin-Darby bovine kidney (MDBK) cells and its comparison with cattle primary cultured hepatocytes

Project description:A reliable hepatic in vitro model is actually needed for pharmacological and toxicological studies in cattle. As established bovine hepatic cell lines are not available, a surrogate stably-transfected cell line could be a good alternative. This data set represent the transcriptomic characterization of the MDBK cells (stably-transfected cell line) in comparison to the present in vitro model of choice; cattle primary cultured hepatocytes. <br>This second part of the study compares hepatocytes vs. liver tissue and is found under E-MTAB-4424.

2017-01-31 | E-MTAB-4430 | biostudies-arrayexpress

Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary wild type and Rad21-cohesin haploinsufficient mouse liver

Project description:Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary mouse liver. The following antibodies were used: CTCF (upstate, 07729), STAG1 (abcam, ab4457), STAG2 (abcam, 4464), RAD21 (abcam, ab992), CEBPA (santa cruz, sc9314), HNF4A (aviva systems biology, ARP31946), FOXA1 (abcam, ab5089), FOXA2 (santa cruz, sc6554), HNF6 (santa cruz, sc13050), HNF1A (santa cruz, sc6547), PREP1 (santa cruz, sc6245), NRSF/REST (santa cruz, sc25398), GABPA (santa cruz, sc22810), E2F4 (santa cruz, sc1082), p300 (santa cruz, sc585), CBP (santa cruz, sc369), RNAP2 (abcam, ab5408), H3K4me1 (abcam, ab8895), H3K4me3 (abcam, ab8580), H3K36me3 (abcam, ab9050), H3K79me2 (abcam, ab3594), H2AK5ac (abcam, 1764)

2012-06-22 | E-MTAB-941 | biostudies-arrayexpress

Human liver homogenate, liver microsomes, low-speed centrifugation pellet and hepatocytes LC-MS/MS from 15 matched donors

Project description:LC-MS/MS-based label-free proteomics of human liver homogenate, human liver microsomes, and human hepatocytes from 15 matched donors used to compare and understand differences in two major in vitro systems used for drug metabolism studies

2021-03-29 | PXD014131 | Pride

Analysis of RNA from primary hepatocytes from hepatocyte-specific SRSF1 knockout mice vs. WT

Project description:RNA from primary hepatocyte cultures from three 3-month-old SRSF1HKO mice compared to RNA from three 3-month-old WT mice for changes in exon utilization and gene expression. SRSF1 KO vs. WT, three replicates each.

2015-05-01 | E-GEOD-57020 | biostudies-arrayexpress

Transcriptome analysis of human sinusoidal endothelial cells, hepatocyte

Project description:We report the transcriptome human primary hepatocytes and liver sinusoidal endothelial cells. Hepatocytes were obtained from commercial sources. LSECs were isolated based on the coexpression of Tie2 and CD32b, te strategy of purification controlled by RNA-Seq. Comparison of the expression of the Tie-2, CD32b, SELP, FVIII, VWF, Alb, Fg, F7genes

2015-01-01 | E-GEOD-43984 | biostudies-arrayexpress

Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 7]

Project description:In this study, we generated genome-wide data sets for four histone modifications, including H3K9ac, H3K27ac, RNA pol II, H3K9me3, which were collected from MDBK cell line before and after (24h) Butyrate treatment. By combining other types of data sets collected in Rumen Epithelial Primary Cells (REPC) , inclduing four histone codes, CTCF, DNA accessibility, DNA methylation, and RNA-seq, we established and validated the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

2019-07-24 | GSE129422 | GEO

Regulation of microRNA expression by rifampin in human hepatocytes

Project description:Rifampin causes drug interactions by altering hepatic drug metabolism. Because microRNAs (miRNAs) have been shown to regulate genes involved in drug metabolism, we determined the effect of rifampin on the expression of hepatic miRNAs. Primary human hepatocytes from seven subjects were treated with rifampin, and the expression of miRNA and cytochrome P450 (P450) mRNAs was measured by TaqMan assays and RNA-seq, respectively. Rifampin induced the expression of 10 clinically important and 13 additional P450 genes and repressed the expression of 9 other P450 genes (P < 0.05). Rifampin induced the expression of 33 miRNAs and repressed the expression of 35 miRNAs (P < 0.05). Several of these changes were highly negatively correlated with the rifampin-induced changes in the expression of their predicted target P450 mRNAs, supporting the possibility of miRNA-induced regulation of P450 mRNA expression. In addition, several other miRNA changes were positively correlated with the changes in P450 mRNA expression, suggesting similar regulatory mechanisms. Despite the interindividual variability in the rifampin effects on miRNA expression, principal components analysis clearly separated the rifampin-treated samples from the controls. In conclusion, rifampin treatment alters miRNA expression patterns in human hepatocytes, and some of the changes were correlated with the rifampin-induced changes in expression of the P450 mRNAs they are predicted to target. Primary human hepatocytes were treated rifampin or vehicle for 24 hours. Rifampin-treated samples are not available for the 30Jul10 patient or the Hep2 patient due to raw data file corruption.

2016-04-06 | E-GEOD-79933 | biostudies-arrayexpress

Adaption of oxidative phosphorylation machinery compensates hepatic lipotoxicity in early stages of MAFLD, isolated mitochondria PMID:3543314

Project description:Mitochondrial function is an important control variable in the progression of metabolic dysfunction associated fatty liver disease (MAFLD). We hypothesize that organization and function of mitochondrial electron transport chain (ETC) in this pathologic condition is a consequence of shifted substrate availability. Paradoxically, in MAFLD increased de novo lipogenesis (DNL) occurs despite hepatic insulin resistance. Therefore, we addressed this question using our animal model alb-SREBP-1c, which exhibits increased DNL by constitutively active SREBP-1c. Using an omics approach, we show that the abundance of ETC complex subunits and metabolic pathways are altered in liver of these animals. Analyses of cellular metabolic status by functional assays revealed that SREBP-1c-forced DNL induces a limitation of substrates for oxidative phosphorylation that is rescued by enhanced complex II activity. Furthermore, energy metabolism associated gene regulation indicates the counteracting to increase expression of mitochondrial genes and features cell communication by miRNA and exosomal RNA transfer. In conclusion, substrate availability fuels mainly complex II electron flows as a consequence of activated DNL with impact on whole body by liver-specific exosomal RNAs in early stages of MAFLD.https://pubmed.ncbi.nlm.nih.gov/35743314/

2022-08-02 | PXD032211 | Pride

RNA-seq of human primary hepatocytes treated with FGF19 and CDCA

Project description:Primary human hepatocytes were treated with recombinant FGF19 (n=3), CDCA (n=3), endogenously produced FGF19 (n=3), or vehicle controls (n=3+3). Total RNA was harvested and sequenced with a strand-specific paired end RNA-seq protocol.

2021-02-13 | E-MTAB-8627 | biostudies-arrayexpress

ChIP-seq analysis of Arid1a and C/ebpÎ± in the mouse livers

Project description:Arid1a is the subunit of SWI/SNF complex, which was reported to guide SWI/SNF to DNA. Here, we found that loss of Arid1a in the liver and other adult tissues results in improved organ regeneration. Within SWI/SNF complexes, Arid1a physically interacts with C/ebpÎ±, a hepatocyte transcription factor that drives maturation and limits proliferation. Genome-wide analysis showed that loss of Arid1a reduces the recruitment and activity of C/ebpÎ± on target promoters, resulting in expression programs that favor regeneration and cellular fitness during injury. Arid1a binding is enriched in promoters near transcriptional start sites (TSSs), and C/ebpÎ± binds at precisely the same positions, indicating that Arid1a facilitates C/ebpÎ± binding across the genome. Perfuse and isolate primary hepatocytes from mice livers, analysis of genomic occupancy of C/ebpÎ± and H3K4me2 in hepatocytes from Arid1a WT and Arid1a liver specific KO mice by ChIP-seq. Analysis of genomic occupancy of Arid1a in the hepatocytes from V5-Arid1a transgenic mouse by ChIP-seq.

2016-03-30 | E-GEOD-65167 | biostudies-arrayexpress

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