MeDIP-seq profiles of mouse ApcDHep hepatocytes at day 6 vs wt hepatocytes
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE239777 | GEO | 2023/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:Five-week old male C57BL/6J mice (20 ± 2 g) were intraperitoneally injected with of 20% CCl4 solution in sterile mineral oil at a dose of 2.5 ml CCl4 per kilogram body weight twice per week for eight weeks. Afterwards, the primary hepatocytes were isolated by pronase/collagenase perfusion digestion followed by subsequent density gradient centrifugation. The isolated primary hepatocytes were counted with a hemocytometer to determine the number and percentage of viable cells using the trypan blue method. The isolated cells with the viability above 90% were used for the experiments.
2024-01-01 | GSE243644 | GEO
Project description:MeDIP-seq profiles of mouse ApcDHep hepatocytes at day 6 vs wt hepatocytes
| PRJNA1000949 | ENA
Project description:Femurs bearing breast metastatases (5-pooled animals per sample) were crushed and digested with 2mg/ml Collagenase A.
2023-03-08 | GSE210286 | GEO
Project description:We investigated the effects of the flutamide (FLU) -induced liver injury in primary rat hepatocytes using our liver microfluidic biochips. Flutamide is used a non-steroidal anti-androgenic drug. Two flutamide concentrations, 10µM and 100µM, were used to expose the hepatocytes for 24h under perfusion.
2013-12-01 | GSE44317 | GEO
Project description:We investigated the effects of the flutamide (FLU) -induced liver injury in primary rat hepatocytes using our liver microfluidic biochips. Flutamide is used a non-steroidal anti-androgenic drug. Two flutamide concentrations, 10M-BM-5M and 100M-BM-5M, were used to expose the hepatocytes for 24h under perfusion. Primary rat hepatocytes were cultivated in microfluidic biochips and treated with 10 and 100M-BM-5M of flutamide for 24h
2013-12-01 | E-GEOD-44317 | biostudies-arrayexpress
Project description:Tumor-bearing mammary fat pads from MMTV-PyMT mice were digested with 2mg/mL Collagenase A and 2U/mL Dnase.
2024-04-29 | GSE229355 | GEO
Project description:Glucocorticoids are widely used therapeutically to suppress inflammatory/immune responses and most of their effects are produced either by altering transcription of specific genes directly, or by altering the expression of transcription factors that subsequently alter the expression of downstream genes. Relevant data from previous studies indicate that the number of genes regulated by glucocorticoid receptor exceeds 4000 in cells and that 358 different genes are regulated in the liver of adrenalectomized males rats treated with a chronic infusion of methylprednisolone for up to 1 week . However, differences in gene expression between males and females in response to glucocorticoid treatment in isolated hepatocytes are not known. Livers were isolated from adult male and female Sprague-Dawley rats and digested with the collagenase perfusion method developed by Berry and Friend (J Cell Biol 43, 506-520;1969). After collagenase treatment, the liver was excised, minced in balanced salt solution, and centrifuged at 50 g for 3 min. Immediately after isolation, hepatocytes were resuspended in Williams E Medium containing penicillin (100 units/ml), streptomycin (100 M-NM-<g/ml), 2 mM glutamine pH 7.4, and 10% fetal bovine serum and plated on collagen-coated 94 x 16 mm cell culture dishes and maintained for 24 hours in a 95% airM-bM-^@M-^S5% CO2, 37M-BM-0C incubator. The medium was then changed to free serum Williams E Medium and maintained in culture for an additional 24 hours. Hepatocytes isolated from male and rats were treated with vehicle (0.01% ethanol) or dexamethasone (100 nm) for 6 hours. Total RNA from cells were extracted by using the RNeasy Midi Kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys instructions. All samples were treated with the RNase-free DNase set (Qiagen) and were kept at -80M-BM-0C until labeling and hybridization.
2010-10-30 | E-GEOD-24255 | biostudies-arrayexpress
Project description:To understand the relationship between protein expression and mRNA translation during primary hepatocytes dedifferentiation, we have employed transcriptome microarrayas a discovery platform. Rat primary hepatocytes were isolated by the method of two-step enzymes perfusion and then cultured on mono-layer in vitro. Samples at 0h( just after perfusion, before planking) , 6h, 12h ,24h and 48h were collected. Integrative analysis of transcriptome and whole cell proteomics (WCP) leaded us to realize the poor correlation of them. This discovery made us realize that targeting mRNA was far from enough in illustrating this process. It would provide new insights from the aspects of post-translational modifications(PTMs).Post-translational modifications play important role in numorous biological and pathological process, but a few reports are related to primary hepatocytes dedifferentiation process, and there is still no integrative proteomics analysis in this field yet. In this study, we perform ubiquitinome phosphorylated proteome, whole cell proteome and transcriptome simultaneously during the five different time points of dedifferentiation in vitro quantified over 6000 modified sites mapping to over 2000 proteins. And comprehensive analysis of these datasets provides novel insight in this field.
2022-09-26 | GSE138071 | GEO
Project description:Purpose: Elucidate the hepatocyte-specific effects of innate antiviral response to a hepatotropic virus. Methods: Hepatocytes were isolated using a standard 2 step perfusion protocol and viable CD45 negative single cells were sorted on a Sony SH800 instrument und subsequently processed using a 10x Genomics Controller according to standard protocols. Results: Hepatocytes upregulate inflammatory genes and downregulate metabolic genes. Conclusion: Hepatocytes are important innate immune signaling platforms in the liver during viral infection.
2019-12-05 | GSE137082 | GEO
Project description:Studies in mice have shown that PPARalpha is an important regulator of hepatic lipid metabolism and the acute phase response. However, little information is available on the role of PPARalpha in human liver. Here we set out to compare the function of PPARalpha in mouse and human hepatocytes via analysis of target gene regulation. Primary hepatocytes from 6 human and 6 mouse donors were treated with PPARalpha agonist Wy14643 and gene expression profiling was performed using Affymetrix GeneChips followed by a systems biology analysis. Baseline PPARalpha expression was similar in human and mouse hepatocytes. Depending on species and time of exposure, Wy14643 significantly induced the expression of 362-672 genes. Surprisingly minor overlap was observed between the Wy14643-regulated genes from mouse and human, although more substantial overlap was observed at the pathway level. Xenobiotics metabolism and apolipoprotein synthesis were specifically regulated by PPARalpha in human hepatocytes, whereas glycolysis-gluconeogenesis was regulated specifically in mouse hepatocytes. Most of the genes commonly regulated in mouse and human were involved in lipid metabolism and many represented known PPARalpha targets, including CPT1A, HMGCS2, FABP, ACSL, and ADFP. Several genes were identified that were specifically induced by PPARalpha in human (MBL2, ALAS1, CYP1A1, TSKU) or mouse (Fbp2, lgals4, Cd36, Ucp2, Pxmp4). Furthermore, several putative novel PPARalpha targets were identified that were commonly regulated in both species, including CREB3L3, KLF10, KLF11 and MAP3K8. Our results suggest that PPARalpha activation has a major impact on gene regulation in human hepatocytes. Importantly, the role of PPARalpha as master regulator of hepatic lipid metabolism is generally well-conserved between mouse and human. Overall, however, PPARalpha regulates a mostly divergent set of genes in mouse and human hepatocytes. Experiment Overall Design: Primary hepatocytes from 6 human subjects were treated with the PPARalpha agonist Wy14643 for 6 and 24 hours, and gene expression profiling was performed using Affymetrix GeneChips. Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%. Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 microM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
2009-09-25 | E-GEOD-17251 | biostudies-arrayexpress