Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,233
datasets available to search
ShareScore release 0.9.0
Dataset results
1,233 results for “Hepatocytes”
dual scRNA-seq analysis of P. vivax infected hepatocytes
<p>Malaria-causing <em>Plasmodium vivax</em> parasites can linger in the human liver for weeks to years, and then reactivate to cause recurrent blood-stage infection. While an important target for malaria eradication, little is known about the molecular features of the replicative and non-replicative states of intracellular <em>P. vivax</em> parasites, or their human host-cell dependencies and the host responses to them. Here, we leverage a bioengineered human microliver platform to culture patient-derived <em>P. vivax</em> parasites in primary human hepatocytes and conduct transcriptional profiling. By coupling enrichment strategies with bulk and single-cell analyses, we captured both parasite and host transcripts in individual hepatocytes throughout the infection course. We define host- and state-dependent transcriptional signatures and identify previously unappreciated populations of replicative and non-replicative parasites, sharing features with sexual transmissive forms. We find that infection suppresses transcription of key hepatocyte function genes, and that <em>P. vivax</em> elicits an innate immune response that can be manipulated to control infection. Our work provides an extendible framework and resource for understanding host-parasite interactions and reveals new insights into the biology of <em>P. vivax</em> dormancy and transmission.</p>
HBV-only reads from cultured human hepatocytes infected with HBV used for testing HBVouroboros functionalities.
<p>The dataset consists of bulk-RNA reads extracted from cultured human hepatocytes infected with HBV. The data is used to test the performance of the HBVouroboros software (https://github.com/bedapub/HBVouroboros).</p> <p>Note that fastq files are comprised of reads that map to HBV genome, as such sample files for negative controls of HBV infection are empty files. We include these for the sake of completeness and to reflect the experimental design.</p>
Data files: Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets
<p>Scripts, preprocessed count matrices, and single-cell data objects generated in <strong>“Single-cell RNA profiling of <em>Plasmodium vivax</em><em>-</em>infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets” </strong></p>
Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in mouse, rat, and pooled human hepatocytes
<p>Like many per- or polyfluorinated alkyl substances (PFAS), toxicity studies with HFPO-DA (ammonium,2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate), a short-chain PFAS used in the manufacture of some types of fluorinated polymers, indicate that the liver is the primary target of toxicity in rodents following oral exposure. Although the current weight of evidence supports the PPARa mode of action (MOA) for liver effects in HFPO-DA-exposed mice, alternate MOAs have also been hypothesized including PPARg or cytotoxicity. To further evaluate the MOA for HFPO-DA in rodent liver, transcriptomic analyses were conducted on samples from primary mouse, rat and pooled human hepatocytes treated for 12, 24 or 72 hours with various concentrations of HFPO-DA, or agonists of PPARa (GW7647), PPARg (rosiglitazone), or cytotoxic agents (i.e., acetaminophen or d-galactosamine). Concordance analyses of enriched pathways across chemicals within each species demonstrated greatest concordance between HFPO-DA and PPARa agonist GW7647-treated hepatocytes compared to the other chemicals evaluated. These findings were supported by benchmark concentration modeling and predicted upstream regulator results. In addition, transcriptomic analyses across species demonstrated a greater transcriptomic response in rodent hepatocytes treated with HFPO-DA or agonists of PPARa or PPARg, indicating rodent hepatocytes are more sensitive to HFPO-DA or PPARa/g agonist treatment. These results are consistent with previously published transcriptomic analyses and further support that liver effects in HFPO-DA-exposed rodents are mediated through rodent-specific PPARa signaling mechanisms as part of the MOA for PPARa activator-induced rodent hepatocarcinogenesis. Thus, effects observed in mouse liver are not appropriate endpoints for toxicity value development for HFPO-DA in human health risk assessment.</p>
Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in wild-type and PPARa knockout mouse hepatocytes
Open the record for dataset details and reuse information.
Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in mouse, rat, and pooled human hepatocytes
Open the record for dataset details and reuse information.
Promoter methylation leads to Hepatocyte Nuclear Factor 4A loss and pancreatic cancer aggressiveness.
<p><i>Efforts to decode pancreatic ductal adenocarcinoma (PDAC) heterogeneity and the consequent therapeutic selection remains a challenge. We aimed to characterize epigenetically regulated pathways involved in PDAC progression.</i></p><p><i>Global DNA methylation analysis in pancreatic cancer patient tissues and cell lines was performed to identify differentially methylated genes. Targeted bisulfite sequencing and in vitro methylation reporter assays were employed to investigate the direct link between sitespecific methylation and transcriptional regulation. A series of in vitro loss- and gain-of function studies, and in vivo xenograft and the KPC (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre) mouse models were used to assess pancreatic cancer cell properties. Gene and protein expression analyses were performed in three different cohorts of pancreatic cancer patients and correlated to clinicopathological parameters.</i></p><p><i>We identify Hepatocyte Nuclear Factor 4A (HNF4A) as a novel target of hypermethylation in pancreatic cancer and demonstrate that site-specific proximal promoter methylation drives HNF4A transcriptional repression. Expression analyses in patients, indicate the methylation-associated suppression of HNF4A expression in pancreatic cancer tissues. In vitro and in vivo studies reveal that HNF4A is a novel tumor suppressor in pancreatic cancer, regulating cancer growth and aggressiveness. As evidenced in both the KPC mouse model and human pancreatic cancer tissues, HNF4A expression declines significantly in the early stages of the disease. Most importantly, HNF4 loss correlates with poor overall patient survival.</i></p>
A novel UPLC-MS metabolomic analysis-based strategy to monitor the course and extent of iPSC differentiation to hepatocytes
<p>ms2 raw data, peak tables generated in Quantitative Analysis Software from Agilent and Matlab functions for QC-SVRC, data clean-up and analysis for the publication with title "Monitoring the differentiation of iPSC to hepatocytes by means of UPLC-MS metabolomics".</p>
Study of Hepatocyte Growth Factor (HGF) Via Plasmid Vector to Improve Perfusion in Critical Limb Ischemia Patients With Peripheral Ischemic Ulcers
ClinicalTrials.gov study NCT00189540. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Hepatocyte Growth Factor to Improve Functioning in PAD
ClinicalTrials.gov study NCT03363165. IPD Sharing: NO. Countries: 1. Publications: 1.
MicroRNA-574-5p targeting HOXC6 expression inhibits the hepatocyte lipid uptake to alleviate NAFLD
<p>In recent times, the non-alcoholic fatty liver disease (NAFLD) is increasing worldwide. Increasing evidence supports the role of miRNAs in the pathogenesis of NAFLD. The miR-574-5p has been shown to be involved in lipid metabolism. However, studies on the correlation between miR-574-5p and NAFLD are lacking. Hence, in this study, we wanted to investigate <strong>whether miR-574-5p is associated with the pathogenesis of NAFLD</strong>. Through various <em>in vivo</em> and <em>in vitro</em> experiments, we found that miR-574-5p can inhibit lipid accumulation and lipid formation by targeting the HOXC6 3' UTR. We believe that our study makes a significant contribution to the literature because <strong>this study is the first to show that miR-574-5p is downregulated in liver tissue in </strong><strong>a</strong><strong> mouse NAFLD model</strong>. Further, understanding the miRNAs and their targets that regulate NAFLD may help us better understand the disease and lead to the design of a potential therapeutic against NAFLD in the future.In recent times, the non-alcoholic fatty liver disease (NAFLD) is increasing worldwide. Increasing evidence supports the role of miRNAs in the pathogenesis of NAFLD. The miR-574-5p has been shown to be involved in lipid metabolism. However, studies on the correlation between miR-574-5p and NAFLD are lacking. Hence, in this study, we wanted to investigate <strong>whether miR-574-5p is associated with the pathogenesis of NAFLD</strong>. Through various <em>in vivo</em> and <em>in vitro</em> experiments, we found that miR-574-5p can inhibit lipid accumulation and lipid formation by targeting the HOXC6 3' UTR. We believe that our study makes a significant contribution to the literature because <strong>this study is the first to show that miR-574-5p is downregulated in liver tissue in </strong><strong>a</strong><strong> mouse NAFLD model</strong>. Further, understanding the miRNAs and their targets that regulate NAFLD may help us better understand the disease and lead to the design of a potential therapeutic against NAFLD in the future.</p>
Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files)
<p>This repository contains raw sequencing data (FASTQ files) produced from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2") . Sequencing libraries were prepared following the latest version of the nanoCAGE protocol (Poulain et al., Methods Mol Biol. 2017;1543:57-109. doi: 10.1007/978-1-4939-6716-2_4). They respectively contain a mix of 24 ("NC_LIMMS") and 18 ("NC_LIMMS2") samples tagged by specific barcode sequences at the 5'-ends (see tables below). The tagmentation step included in the protocol was performed using an equimolar mix of 12 Nextera XT N-series index primers (N701 to N712), therefore "NNNNNNNN" was indicated as index sequence on the Illumina Sample Sheet for the demultiplexing (see tables below). Libraries were sequenced paired-end on Illumina MiSeq system with the MiSeq Reagent Kit v3 (150 cycles: 58 cycles used for READ1, 8 cycles used for the Index, and 84 cycles used for READ2). Genomic alignments (BED files) of paired-end reads on human genome assemblies hg19 and hg38 using the MOIRAI pipeline (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1017276.</p> <p> </p> <p><em><strong>"170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") :</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>1 iPSC_control_rep1 4 ACAGAT NNNNNNNN</p> <p>2 iPSC_control_rep2 24 ATCGTG NNNNNNNN</p> <p>3 iPSC_control_rep3 31 CACGAT NNNNNNNN</p> <p>4 S3P1_OK_rep1 36 CACTGA NNNNNNNN</p> <p>5 S3P1_OK_rep2 46 CTGACG NNNNNNNN</p> <p>6 S3P1_OK_rep3 63 GAGTGA NNNNNNNN</p> <p>7 S4P1_OK_rep1 79 GTATAC NNNNNNNN</p> <p>8 S4P1_OK_rep2 92 TCGAGC NNNNNNNN</p> <p>9 S4P1_OK_rep3 9 ACATGA NNNNNNNN</p> <p>10 S4P2_OK_rep1 21 ATCATA NNNNNNNN</p> <p>11 S4P2_OK_rep2 33 CACGTG NNNNNNNN</p> <p>12 S4P2_OK_rep3 45 CGATGA NNNNNNNN</p> <p>13 S1P1_rep1 57 GAGATA NNNNNNNN</p> <p>14 S1P1_rep2 69 GCTCTC NNNNNNNN</p> <p>15 S1P1_rep3 81 GTATGA NNNNNNNN</p> <p>16 S3P1_FAILED_rep1 93 TCGATA NNNNNNNN</p> <p>17 S3P1_FAILED_rep2 11 AGTAGC NNNNNNNN</p> <p>18 S3P1_FAILED_rep3 23 ATCGCA NNNNNNNN</p> <p>19 S4P1_FAILED_rep1 35 CACTCT NNNNNNNN</p> <p>20 S4P1_FAILED_rep2 47 CTGAGC NNNNNNNN</p> <p>21 S4P1_FAILED_rep3 59 GAGCGT NNNNNNNN</p> <p>22 S4P2_FAILED_rep1 71 GCTGCA NNNNNNNN</p> <p>23 S4P2_FAILED_rep2 83 TATAGC NNNNNNNN</p> <p>24 S4P2_FAILED_rep3 95 TCGCGT NNNNNNNN</p> <p> </p> <p><em><strong>"180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"):</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>25 PETRI_rep1 04 ACAGAT NNNNNNNN</p> <p>26 PETRI_rep2 24 ATCGTG NNNNNNNN</p> <p>27 PETRI_rep3 31 CACGAT NNNNNNNN</p> <p>28 BIOCHIP_E_rep1 6 CACTGA NNNNNNNN</p> <p>29 BIOCHIP_M_rep1 46 CTGACG NNNNNNNN</p> <p>30 BIOCHIP_S_rep1 63 GAGTGA NNNNNNNN</p> <p>31 BIOCHIP_E_rep2 79 GTATAC NNNNNNNN</p> <p>32 BIOCHIP_M_rep2 92 TCGAGC NNNNNNNN</p> <p>33 BIOCHIP_S_rep2 09 ACATGA NNNNNNNN</p> <p>34 BIOCHIP_E_rep3 21 ATCATA NNNNNNNN</p> <p>35 BIOCHIP_M_rep3 33 CACGTG NNNNNNNN</p> <p>36 BIOCHIP_S_rep3 45 CGATGA NNNNNNNN</p> <p>37 HEPATOCYTES_rep1 57 GAGATA NNNNNNNN</p> <p>38 HEPATOCYTES_rep2 69 GCTCTC NNNNNNNN</p> <p>39 iPSC_control_rep1-2 81 GTATGA NNNNNNNN</p> <p>40 BIOCHIP_E_rep2-2 93 TCGATA NNNNNNNN</p> <p>41 BIOCHIP_M_rep1-2 11 AGTAGC NNNNNNNN</p> <p>42 BIOCHIP_S_rep2-2 23 ATCGCA NNNNNNNN</p>
Underlying data for "Metabolism of remimazolam in primary human hepatocytes during continuous long-term infusion in a 3D bioreactor system"
<p>The dataset supports the manuscript "Metabolism of remimazolam in primary human hepatocytes during continuous long-term infusion in a 3D bioreactor system" published in the journal "Drug design, development and therapy" in 2019</p>
Primary hepatocyte culture from Oreochromis niloticus fish as a tool for environmental toxicology
<p>Accumulated chemicals have been impairing water quality over decades of human activities. Organisms such as fish are often used for risk assessment, as chemical analysis is insufficient to assess the impact on health. Consequently, researchers have faced challenges in ecotoxicology, concerning the use of animals. Primary and cell line cultures are good alternatives for reducing animal use. This study aims to evaluate the use of primary hepatocytes culture from Oreochromis niloticus as an in vitro tool for screening environmental contaminants and pollutants. Metal cadmium (Cd) is the pollutant model.</p>
Hepatocyte Transplantation for Liver Based Metabolic Disorders
ClinicalTrials.gov study NCT01345578. IPD Sharing: UNDECIDED. Countries: 1. Publications: 6.
Pulmonary and Systemic Hepatocyte Growth Factors in Patients With COPD
ClinicalTrials.gov study NCT00477074. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Hepatocyte Matrix Implant Study Indonesia
ClinicalTrials.gov study NCT01335568. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Hepatocyte Transplantation for Acute Decompensated Liver Failure
ClinicalTrials.gov study NCT01345565. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Micro-encapsulated Hepatocyte Intraperitoneal Transplantation in Liver Failure Adults
ClinicalTrials.gov study NCT05727722. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Vascular Endothelial Growth Factor (VEGF), Platelet Derived Growth Factor (PDGF), Hepatocyte Growth Factor (HGF) in Patients With Acute Coronary Syndrome (ACS)
ClinicalTrials.gov study NCT00844987. IPD Sharing: Not stated. Countries: 1. Publications: 3.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.