Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human liver cancer cell lines after lncRNA overexpression with CRISPRa

ABSTRACT: Biological replicates of Human liver cancer cell line Huh7 (n = 2-4) were treated with CRISPRa to overexpress (OE) LINC00326, LINC01419, LINC02119, novel lncRNAs MSTRG.12891, as well as and non-targeting (NT) control. Cells were harvested 48hrs after transfection. Total RNA was extracted and sequenced with a strand-specific paired end RNA-seq protocol.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Jonas Søndergaard

PROVIDER: E-MTAB-9586 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNA-seq of human liver cancer cell lines after RBP-KD

Project description:Biological replicates of Human liver cancer cell lines HepG2 (n = 2) and Huh7 (n = 2) were treated with siRNA (KD) against CCT3, DDX39A, TOP2A, PKM, STMN1, HIST1H1C, NQO1, KPNA2, PEG10, IGF2BP1, and non-targeting (NT) control. Cells were harvested 48hrs after transfection. Total RNA was extracted and sequenced with a strand-specific paired end RNA-seq protocol.

2021-12-23 | E-MTAB-9587 | biostudies-arrayexpress

In vitro RIP-seq for Zfp207 in mouse embryonic stem cells

Project description:in vitro RIP-seq assay of tagged Zfp207 performed in 2 technical replicates with Tag only and Input as negative controls. The input RNA used for the assay is total RNA extracted from mESC. The data provides information about the transcripts and the binding sites that Zfp207 has in the transcriptome of mESC

2021-12-09 | E-MTAB-10113 | biostudies-arrayexpress

RNA Affinity Purification followed by sequencing (RAP-seq) allows identification of transcriptome-wide RBP binding sites using recombinant RBPs and total purified cellular RNA

Project description:RAP-seq is a new method that provides in vitro derived RNA-Interactomes for any given RBP. In RAP-seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP-Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study, RAP-seq was used to identify RNA-Interactomes of 26 novel RBPs (aka non-canonical RBPs) newly discovered in proteome-wide studies as RNA binders. RAP-seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1, IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome-wide changes in their RNA Interactomes with respect to the wild-type IGF2BPs were reported. Also a transcriptome-wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition, a tipical RAP-seq substrate (fragmented total RNA) if reverse-transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP-seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome-wide binding events for YTHDF1, hence with RAP-seq we also report T7-RAP-seq.

2023-09-13 | E-MTAB-10834 | biostudies-arrayexpress

MicroRNAs are Transported in Plasma and Delivered to Recipient Cells by High-Density Lipoproteins (HG-U133 2.0)

Project description:Circulating microRNAs (miRNA) are relatively stable in plasma and are a new class of disease biomarkers. Here we present evidence that human high-density lipoprotein (HDL) transports endogenous miRNAs and delivers them to recipient cells with functional targeting capabilities. Highly-purified fractions of human HDL contain small RNAs, and the HDL-miRNA profile from normal subjects is significantly different than familial hypercholesterolemia subjects. miRNAs were demonstrated to associate with both native and reconstituted HDL particles, and reconstituted HDL injected into mice retrieved distinct miRNA profiles from normal and atherogenic models. Cellular export of miRNAs to HDL was demonstrated to be regulated by neutral sphingomyelinase. HDL-mediated delivery of miRNAs to recipient cells was demonstrated to be scavenger receptor BI-dependent. Furthermore, HDL delivery of both exogenous and endogenous miRNAs resulted in the direct targeting of mRNA reporters. Notably, HDL-miRNA from atherosclerotic subjects induced differential gene expression, with significant loss of conserved mRNA targets in cultured hepatocytes. Collectively, these observations suggest that HDL participates in a novel mechanism of intercellular communication involving the transport and delivery of miRNAs. Gene expression changes in human Huh7 cells with familial hypercholesterolemia HDL treatment. Gene expression (mRNA) profiles in human Huh7 cells treated with normal HDL (n=3) or FH HDL (n=3) in lipoprotein-depleted serum (48h).

2011-03-24 | E-GEOD-25311 | biostudies-arrayexpress

Proteomic analysis of vocal fold fibroblasts exposed to cigarette smoke extract

Project description:Reinke’s edema is a cigarette associated, benign, mostly bilateral lesion of the vocal folds leading to dysphonia and dyspnea. Until today information about pathophysiology is only scarce, treatment is only surgical. To explore the pathophysiology of Reinke’s edema, we exposed near primary human vocal fold fibroblasts to cigarette smoke extract enriched medium or air bubbled control for 24 hrs. followed by a proteomic analysis. Proteomic analyses revealed an increase of proteins involved in oxidative stress response. We furthermore found that a significant number of essential extracellular matrix proteins was altered by culturing human VFF with CSE enriched medium: UDP-glucose 6-dehydrogenase, a protein involved in hyaluronan synthesis was upregulated, while the expression of several fibrillar collagen types was significantly reduced. The current findings corroborate previous studies but revealed new insights in possible disease mechanisms of Reinke’s edema too. We postulate that changes in the composition -reduction of collagen fibrils, increase of hyaluronan- of the vocal folds’ ECM may lead to the clinical findings.

2019-08-06 | PXD010640 | Pride

Chromatin accessibility in human monocytes differentiation (3D-MO)

Project description:This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 39 samples.

2022-06-24 | E-MTAB-10846 | biostudies-arrayexpress

RNA-seq of human plasma microRNAs in Alzheimer Disease

Project description:MicroRNAs (miRNAs) could play an important role as potential Alzheimer Disease (AD) biomarkers. Plasma samples were collected from participants: Mild cognitive impairment (MCI) due to AD patients (n= 20), preclinical AD patients (n= 8) and healthy controls (n= 20). Then, small RNA sequencing analysis, followed by miRNA differential expression analysis comparing different methods (DESeq2, edgeR, NOISeq) were carried out.

2022-05-08 | E-MTAB-11103 | biostudies-arrayexpress

Prolyl hydroxylation is required for maturation and secretion of Zika virus non-structural protein 1

Project description:Mosquito-borne flaviviruses such as Zika virus (ZIKV) and dengue virus (DENV) have a high epidemic potential and are associated with a wide range of possible outcomes, from asymptomatic infections to severe complications. The flavivirus non-structural protein 1 (NS1), which can be membrane-bound as well as secreted from the cell, plays important roles in viral replication, immune evasion and pathogenesis. To identify the interactome of ZIKV NS1, we infected Huh7 and neural progenitor cells with recombinant ZIKV encoding a FLAG-tagged NS1 and analysed the binding partners with quantitative mass spectrometry. In both cell types, multiple prolyl hydroxylase enzymes were identified as NS1 interactors and mass spectrometry data showed that NS1 contains potential hydroxyproline residues at positions 181, 267 and 281, indicating that these enzymes are involved in post-translational modification of NS1. Chemical inhibition of prolyl hydroxylase enzymes reduced ZIKV RNA levels and titers, as well as NS1 glycosylation, plasma membrane localization and secretion. Mutagenesis of the proline residue at position 281 moderately impaired proper expression of NS1, although viral replication was unaffected. In contrast, substituting proline at position 267 strongly dysregulated NS1 expression and reversions to the wild-type sequence were observed already after passage 1, suggesting that this mutation leads to severe replication defects. Our results identify prolyl hydroxylation as an essential post-translational modification of ZIKV NS1.

2025-01-28 | PXD041488 | Pride

Analysis of human enteroids and colonoids (3D organoid models from small intestine and colon) exposed to chemotherapy agent and tyrosine kinase inhibitor (TKI) gefitinib sampled at four doses (0.1, 1, 10 and 30uM) and at three time points (24, 48 and 72h) since initial exposure

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of gefitinib on 3D human organoid cultures derived from small intestine and colon segments. Experiments were conducted with a dose (0.1, 1, 10 and 30uM of gefitinib) and time series regimen (24, 48 and 72h). Time-matched controls (DMSO 0.1% and medium only) were also included. This dataset is part of the TransQST collection.

2022-04-11 | E-MTAB-11221 | biostudies-arrayexpress

Analysis of mouse enteroids and colonoids exposed to chemotherapy agent 5-fluorouracil (5FU)

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of 5FU on 3D mouse organoid cultures derived from small intestine and colon segments. Experiments were conducted in a dose-repeated (daily media refreshing with 10, 100 or 1000 uM of 5FU) and time series regimen (24, 48 and 72h). Time-matched controls (DMSO 0.1% and medium only) were measured, as well as a baseline exposure prior to the beginning of the exposures (medium only, 0h).

2023-09-29 | E-MTAB-9119 | 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