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 analysis of SKOV3 ovarian cancer cell line strains S1 and S2 under 2D and 3D culture conditions

ABSTRACT: This experiment investigates transcriptomic differences between two SKOV3 ovarian cancer cell strains, S1 (CW1) and S2 (SM), to assess how clonal evolution and culture conditions influence gene expression. Bulk RNA sequencing (RNA-seq) was performed on cells cultured in both 2D monolayers and 3D spheroids. The study aims to identify differentially expressed genes and pathways associated with epithelial-mesenchymal transition (EMT), proliferation, and metabolic regulation. The sequencing data were processed using standard bioinformatics pipelines, including quality control, alignment, normalization, and differential expression analysis.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Egle Zymantaite

PROVIDER: E-MTAB-14870 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of mouse EO771 triple-negative breast cancer model with stemness inhibitors: salinomycin, SB-431542, JIB-04, napabucasin, and their quadruple combination against an untreated control

Project description:We conducted an in vivo study of stemness inhibitors using the EO771 triple-negative breast cancer mouse model. Ten days after subcutaneous injection of 1 million of EO771 cells into 8-12 week C57BL/6 female mice right flank, tumors reached around 100-200 mm³. Each treatment group (n=2-3 per group) received three doses of stemness inhibitors (every 3 days) in monotherapy (A - salinomycin, B - SB-431542, C - JIB-04, D - napabucasin) or combination therapy (ABCD). Control mice were left untreated. Tumors were harvested one day after the last treatment and subjected to bulk RNA-seq. This study aims to identify if treatment with stemness inhibitors affected the immune tumor microenvironment in this model.

2025-03-12 | E-MTAB-14915 | biostudies-arrayexpress

Bulk RNA Barcoding and sequencing (BRB-seq) of Mock, ICV, and IDV infected airway epithelial cell cultures of human, porcine, and bovine origin at 33°C and 37°C

Project description:For the assessment of host response dynamics to ICV and IDV infections in human, porcine, and bovine airway epithelial cells at ambient temperature corresponding to the upper or lower respiratory tract. We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq), which allows a rapid and sensitive genome-wide transcriptomic analysis in a highly multiplexed manner. Transcriptome data from human, procine, and bovine was obtained from a total of 3 biological donors for pairwise comparisons of ICV and IDV virus-infected to unexposed AEC cultures at respective time points and temperatures.

2022-07-13 | E-MTAB-11939 | biostudies-arrayexpress

BRBseq performed on 786-O cells treated with 2 inhibitors of protein kinase CK2, CX4945 and AB668

Project description:786-O cells (150, 000) were treated for 24h with DMSO, 5 µM of CX4945 or AB668. Total RNA was extracted from treated cells using the MirVana PARIS kit (Thermofisher). The 3′ Bulk RNA Barcoding and sequencing (BRB-seq) experiments were performed at the Research Institute for Environmental and Occupational Health (Irset, Rennes, France) according to the published protocol (Alpern et al., 2019). Sequencing was perfomred by SiLicium.

2023-05-27 | E-MTAB-12776 | biostudies-arrayexpress

BRBseq performed on tumoroids and corresponding renal tumor tissues

Project description:To evaluate genetic similarities between tumoroids and the corresponding tumor tissues, we performed RNA sequencing of cells for each experimental condition. Since we injected human cancer cells into mice, cancer cells in the tumors were human while microenvironmental cells (i.e. Fibroblasts, Immune cells,…) were derived from mice. Thus, the RNA sequencing datasets generated from ACHN or 786-O tumor tissues (AxM and 7xM) and their respective tumoroids (AxTy and 7xTy) were mapped on human and mouse reference genome.

2023-06-30 | E-MTAB-12928 | biostudies-arrayexpress

Wing disc transcriptomic variation from 32 Drosophila genetic reference panel (DGRP) lines selected for a broad range of wing sizes

Project description:We performed RNA sequencing of wing discs at the wandering L3 larval stage from 32 inbred lines of Drosophila genetic reference panel (DGRP) that consists of 16 big and 16 small wing lines. We aimed to understand system-wide gene regulatory mechanisms that attain the observed natural variation in wing size including the sexual size dimorphism.

2019-02-18 | E-MTAB-7662 | biostudies-arrayexpress

Cooperative blockade of CK2 and ATM kinases drives apoptosis in VHL-deficient renal carcinoma cells / RNA-seq (BRB-seq) of treated 786-O spheroids

Project description:Multicellular Tumor Spheroids (MCTS) were pre-formed for 3 days with 786-O cell line to better mimic the tumor microenviroenment. These spheroids were treated with either vehicle (DMSO), drugs alone (KU-60019 10 μM; CX-4945 5 μM) or in combination (KU + CX) for 48h before RNA extraction.

2021-02-04 | E-MTAB-9977 | biostudies-arrayexpress

Single-cell RNA sequencing of colorectal cancer

Project description:We profile single cells from patients with colorectum cancer using Chromium 3’ and 5’ single-cell RNA-sequencing. Patients EXT001, EXT009, and EXT012 from the KUL dataset were first analyzed by Lee et al., 2020, and the raw data are available in ArrayExpress under the accession codes E-MTAB-8410 and E-MTAB-8107. Patients EXT018, EXT048, EXT113, and EXT121 from KUL dataset were previously analyzed by Joanito et al., 2022. The raw data of those patients are available in EGA under the accession codes EGAD00001008584 and EGAD00001008585.

2022-09-16 | E-MTAB-9934 | biostudies-arrayexpress

3' RNA-seq of differentiating (brown) mouse subcutaneous SVF cells upon knockdown of Zfp521, Fhl1, or Mxd1

Project description:White fat browning is a highly variable genetic trait in mice (Guerra et al., 1998). To gain an overview of strain variations in browning capacities, we performed transcriptome analysis of white fat browning in (1) 5 inbred mouse strains (C57BL/6J, 129S6sv/ev, A/J, AKR/J, and SWR/J) with distinct browning propensities in WAT, and (2) F1 hybrids derived from a high (129S6sv/ev) and low browning strain (C57BL/6J) cross. From our analyses, several transcription factors emerged as novel regulators of white fat browning, including the TFs Zfp521, Fhl1, and Mxd1. We further validated the role of these TFs and performed 3' RNA-seq experiments upon their knockdown, in order to characterize their mechanism of action.

2019-11-01 | E-MTAB-8343 | biostudies-arrayexpress

ATAC-seq of iPSC and human dermal fibroblasts

Project description:ATAC-seq of iPSC and human dermal fibroblasts, used to compare open chromatin and transcription signal.

2021-05-02 | E-MTAB-10381 | biostudies-arrayexpress

Single-cell RNA sequencing of self-maintaining lamina propria macrophages

Project description:Single-cell RNA sequencing of 697 YFP+ CD64+ lamina propria macrophages isolated from Cx3cr1CreERT2.Rosa26-LSL-YFP mice 35 weeks after tamoxifen administration

2018-07-30 | E-MTAB-6976 | 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