Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: error-corrected Next Generation Sequencing of TK6 cells co-cultured with primary hepatocytes liver-on-chip

PROVIDER: PRJNA989178 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25073205_1.fastq.gz	Fastqsanger.gz
	SRR25073205_2.fastq.gz	Fastqsanger.gz
	SRR25073206_1.fastq.gz	Fastqsanger.gz
	SRR25073206_2.fastq.gz	Fastqsanger.gz
	SRR25073207_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Qualifying a human Liver-Chip for predictive toxicology: Performance assesment and economic implications

Project description:We assess RNA expression in human primary hepatocytes in Liver-Chips on Day 3 and Day 5. The hepatocytes were co-cultured in Liver-Chip model with Kupffer cells, Liver sinusoidal endothelial cells (LSECs) and stellate cells .

2025-01-21 | GSE194147 | GEO

Qualifying a human Liver-Chip for predictive toxicology: Performance assessment and economic implications

Project description:We assess RNA expression in human primary hepatocytes in Vials Day 0 and Liver-Chips on Day 3 and Day 7 for two different donors. The hepatocytes were co-cultured in Liver-Chip model with Kupffer cells and Liver sinusoidal endothelial cells (LSECs) and stellate cells .

2022-10-14 | GSE207339 | GEO

Genome-wide transcriptome profiling of human Liver-Chip model of alcohol-associated liver disease (ALD) using RNA-seq.

Project description:The goal of this study was to assess RNA expression in human primary hepatocytes in response to ethanol exposure compared to control. The hepatocytes were cultured in co-culture on a Liver-Chip model with Kupffer cells and Liver sinusoidal endothelial cells (LSECs) and treated with 0.08% to 0.16% ethanol for 48h.

2021-05-25 | GSE175396 | GEO

Project description:Error-corrected Duplex Sequencing of TK6 cells exposed to 4-nitroquinoline 1-oxide

| PRJNA1192975 | ENA

Project description:Error-corrected Duplex Sequencing of human TK6 cells exposed to N-ethyl-N-nitrosourea

| PRJNA909196 | ENA

RNA-seq of hepatocytes obtained through step-wise differentiation of hIPSCs from a patient with A1AT deficiency and its point mutation-corrected isogenic hIPSC line. Comparison to primary hepatocytes from a healthy donor and an A1AT-deficient patient.

Project description:A1AT deficiency is an autosomal not recessive disorder caused by mutations in the SERPINA1 gene. Individuals with the Z variant retain polymerised protein in the endoplasmic reticulum of hepatocytes, predisposing them to liver disease. This study primarily aimed to uncover the molecular mechanisms that link protein misfolding to liver injury. To that end, RNA was extracted from hepatocytes differentiated from hIPSCs carrying the Z variant and mutation-corrected hIPSCs (control). The second objective of the study was to benchmark the gene expression profile of both hIPSC-derived hepatocytes types to primary hepatocytes of wild type and a Z variant A1AT genotype.

2018-06-26 | E-MTAB-6781 | biostudies-arrayexpress

Next-gen sequencing for miRNA content of exosomes and hepatocytes in mice with acetaminophen toxicity

Project description:Micro RNA content of extracellular vesicles/exosomes may serve as a marker of certain pathophysiological conditions. We report differential expression of micro RNA in exosomes isolated from mouse blood or medium of cultured primary mouse hepatocytes versus parental hepatocytes or whole liver. Studies included exosomes from blood of mice or medium of cultured primary hepatocytes with acetaminophen toxicity as well as a potentially therapeutic cytokine with acetaminophen.

2019-12-02 | GSE77554 | GEO

UNG shapes the specifity of AID-induced somatic hypermutation in non B cells

Project description:Secondary diversification of antibodies through somatic hypermutation (SHM) and class switch recombination (CSR) is a critical component of the immune response. Activation-induced deaminase (AID) initiates both processes by deaminating cytosine residues in immunoglobulin genes. The resulting U:G mismatch can be processed by alternative pathways to give rise to a mutation (SHM) or a DNA double-strand break (CSR). Central to this processing is the activity of uracil-N-glycosylase (UNG), an enzyme normally involved in error-free base excision repair. We used next generation sequencing to analyze the contribution of UNG to the resolution of AID-induced lesions. Loss- and gain-of-function experiments showed that UNG activity can promote both error-prone and high fidelity repair of U:G lesions. Unexpectedly, the balance between these alternative outcomes was influenced by the sequence context of the deaminated cytosine, with individual hotspots exhibiting higher susceptibility to UNG-triggered error-free or error-prone resolution. These results reveal UNG as a new molecular layer that shapes the specificity of AID-induced mutations and may provide new insights into the role of AID in cancer development. Next Generation Sequencing analysis of mutations introduced by AID in non B cells. NIH-3T3 cells were co-transduced with mOrangeSTOP and AID-ERM-bM-^@M-^Sexpressing vectors, together with Ugi (UNG inhibitor), UNG, or empty vector as control (n=3). Transduced cells were cultured in the presence of OHT during 11 d. AID-E58Q-ER vector (catalytically inactive form of AID) was used as a negative control in combination with the previously described constructions (n=3).

2012-07-04 | E-GEOD-39108 | biostudies-arrayexpress

Hepatocytes :MH vs. ProliHH vs. PHH vs. HLC

Project description:Hepatocytes isolated from DILI patient's liver (#2064) were cultured for a long term using irrMEF and EMUKK-05, and comprehensive gene expression was compared between Puromycin-treated and non-treated groups. In addition, comprehensive gene expression analysis of human mature hepatocytes, primary cultured cells, and ips cell-derived hepatocyte-like cells were performed as controls. Two-condition experiment, Proliferating hepatocytes (ProilHH) vs. puromycin-treated ProliHH. Primary human hepatocytes (PHH) and isolated humen mature hepatocytes (MH) and human iPSC-derived hepatocyte-like cells (HLC) as controls.

2021-12-30 | GSE192653 | GEO

scRNA-seq analysis of human iPSC derived Hepatocyte organoids (iHOs) [scRNA-seq]

Project description:Liver has abundant regenerative capacity, but hepatocytes cannot be cultured long-term in vitro. Activation of FXR signaling induced iHOs with both hepatocyte traits and proliferative potential. To investigate the transcriptomic analysis of iHOs, we performed bulk RNA-seq analysis of organoids in different passages and single cell RNA-seq analysis of iHOs. Compared to 2D-iPS-Heps and organoids in other culture conditions, iHOs have expression profiles more similar to primary human hepatocytes and human fetal liver cells. Single cell RNA-seq revealed iHOs have a fraction that co-expresses hepatocyte markers and proliferation markers.

2025-05-13 | GSE247961 | 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