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Splicing of polyA transcripts in Hep3B cells

ABSTRACT: We were interested in identifying novel splice junctions in Hep3B cells, especially in genes involved in cholesterol metabolism like HMGCR, so we sequenced polyA-tailed RNA from Hep3B cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57666 | GEO | 2014/05/15

SECONDARY ACCESSION(S): PRJNA247478

REPOSITORIES: GEO

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Splicing of polyA transcripts in Hep3B cells

Project description:We were interested in identifying novel splice junctions in Hep3B cells, especially in genes involved in cholesterol metabolism like HMGCR, so we sequenced polyA-tailed RNA from Hep3B cells. 1 polyA-selected RNA sample was sequenced from Hep3B cells

2014-05-15 | E-GEOD-57666 | biostudies-arrayexpress

Differential gene expression in Hep3B and Hep3B SOX4-/- cells

Project description:Overexpression of SOX4 in various kinds of cancers specimen was associated with poor prognosis of patients; however, the role of SOX4 in angiogenesis or tumor microenvironment modulation remains unclear. Therefore the endogenous SOX4 was knockout and the differential gene expression between Hep3B and Hep3B SOX4-/- cells were examined via genechip. We found that the differentially expressed genes, EzH2, a SOX4-associated partner, and CXCL12, were repressed in Hep3B SOX4-/- cells compared with parental Hep3B; these results were further assessed via qRT-PCR in Hep3B SOX4-/- versus Hep3B cells.

2020-12-01 | GSE141909 | GEO

Knock-down of all HIF3A splice variants under 1 % hypoxia by siRNA targeting a shared region in Hep3B cells

Project description:The human HIF3A gene undergoes extensive alternative splicing resulting in seven known isoforms. The short splice variant, HIF-3alpha4, is an inhibitor of the hypoxia response driven by HIF-1 and HIF-2. The role of the long isoforms remains unclear. We used cDNA microarray to study the overall impact of HIF3A knock-down by transfecting Hep3B cells with siRNA targeting a region shared by all splice variants under 1 % hypoxia.

2019-12-31 | GSE128846 | GEO

Differential gene expression in Hep3B and Hep3B SOX4-/- cells

Project description:Differential gene expression in Hep3B and Hep3B SOX4-/- cells

| PRJNA595153 | ENA

Overexpression of the long Hypoxia inducible factor (HIF)-3a2 splice variant under 1 % hypoxia in Hep3B cells

Project description:The human HIF3A gene undergoes extensive alternative splicing resulting in seven known isoforms. The short splice variant, HIF-3alpha4, is an inhibitor of the hypoxia response driven by HIF-1 and HIF-2. The role of the long isoforms remains unclear. We used cDNA microarray to study the overall impact of HIF-3a2 overexpression in Hep3B cells under 1 % hypoxia.

2019-12-31 | GSE128845 | GEO

RNA-Seq in Hep3B-shNC and Hep3B-shlnc-CTHCC cells

Project description:RNA-Seq in Hep3B-shNC and Hep3B-shlnc-CTHCC cells

| PRJNA674827 | ENA

RNA seq data of Hep3B-control, Hep3B-sertraline, Hep3B-XL413, Hep3B-XL413-sertraline, Huh7-control, Huh7-sertraline, Huh7-XL413, Huh7-XL413-sertraline cells

Project description:RNA seq data of Hep3B-control, Hep3B-sertraline, Hep3B-XL413, Hep3B-XL413-sertraline, Huh7-control, Huh7-sertraline, Huh7-XL413, Huh7-XL413-sertraline cells

| PRJNA496576 | ENA

Transcription profiling of human Hep3B cells transfected with L1CAM

Project description:To compare the transcription profiling between empty vector transfected Hep3B and L1CAM transfected Hep3B

2011-08-01 | E-MEXP-1357 | biostudies-arrayexpress

Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts

Project description:Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORF), six novel ORF-containing transcripts, and fifteen transcripts encoding for messages that potentially alter protein functions through truncations or fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Of these, an evolutionary conserved protein was detected containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.

2022-08-30 | PXD034464 | Pride

Genetic changes of Hep3B cells after acquired resistance to sorafenib

Project description:In order to explore the genetic changes of Hep3B cells after resistance to sorafenib, we used a dose-increasing method to obtain drug-resistant cell lines from parental Hep3B cells by intermittent stimulation with sorafenib.

2023-12-09 | GSE248769 | GEO

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