Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA seq of human breast cancer cell line MDAMB231 with knockdown of splicing factors SRSF7 and SMNDC1

ABSTRACT: Deep RNA sequencing was performed to investigate the transcriptomic effects of siRNA-mediated knockdown of SRSF7 or SMNDC1 in the triple-negative breast cancer cell line MDA-MB-231. A total of 30 million cells MDA-MB-231 cells were seeded in 6-well plates. The following day, cells were transfected with siKinasePool siRNAs targeting SRSF7, SMNDC1, or a mock control. Samples from three biological replicates were collected 72 hours after transfection. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Stranded PolyA-selected libraries were prepared and sequenced on the DNBseq platform, generating 150-bp paired-end reads on a DNBSEQ-G400 sequencer (BGI Europe).

INSTRUMENT(S): DNBSEQ-G400

ORGANISM(S): Homo sapiens

SUBMITTER: Jurjun Velde

PROVIDER: E-MTAB-16601 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of human breast cancer cell line MDA-MB-231 treated with T025 against untreated controls

Project description:Deep RNA sequencing was performed to investigate the impact of CLKs inhibitor, T-025, on RNA splicing in triple-negative breast cancer cell lines. A total of 30 million MDA-MB-231 cells were seeded in a 6-well plate. The following day, cells were treated with 1 µM T-025 or 0.1% DMSO as negative control for 24 hours. Samples from 3 biological replicates were used. Total RNA was isolated using the RNeasy plus mini kit (Qiagen). Stranded PolyA-selected libraries were prepared using the DNBseq platform, and 100 M 150-bp paired-end reads were sequenced on a DNBSEQ-G400 sequencer by BGI Europe. The differentially expressed genes (DEGs) and alternative splicing events (ASEs) were analyzed to unravel the transcriptomic changes in TNBC cells upon T-025 treatment.

2026-01-01 | E-MTAB-14664 | biostudies-arrayexpress

Time-series RNA-seq reads of MDA-MB-231 cells treated with 100nM doxorubicin

Project description:MDA-MB-231 breast cancer cells were treated with 100 nM doxorubicin for 24h and observed over time in order to elucidate the biological processes of phenotypical adaptation involved in chemoresistance development and identify potential novel targets for future combination therapies.

2026-01-12 | E-MTAB-16509 | biostudies-arrayexpress

Regulation of gene expression in MDAMB231 breast cancer cells by Parvin-beta in 2D vs 3D culture conditions

Project description:Parvin-beta is a focal adhesion protein downregulated in human breast cancer cells. Loss of Parvin-beta contributes to increased integrin-linked kinase activity, cell-matrix adhesion, and invasion through the extracellular matrix in vitro. The effect of ectopic Parvin-beta expression on the transcriptional profile of MDA-MB-231 breast cancer cells, which normally do not express Parvin-beta was evaluated. Particular emphasis was placed upon propagating MDA-MB-231 breast cancer cells in three-dimensional culture matrices. Gene expression profiles of vector control and Parvin-beta transfected MDA-MB-231 cells cultured on (A) monomeric type I collagen coated plastic, (B) embedded in a type I collagen gel, and (C) embedded in basement membrane (growth factor reduced Matrigel), were compared. Interestingly, Parvin-beta re-expression in MDA-MB-231 cells increased the mRNA expression, serine 82 phosphorylation (mediated by CDK9), and activity of the nuclear hormone receptor, peroxisome proliferator-activated receptor gamma (PPARgamma) and a concomitant increase in lipogenic gene expression as a downstream effector of PPARgamma. Importantly, Parvin-beta suppressed breast cancer growth in vivo with associated decreased proliferation. These data suggest that Parvin-beta might influence breast cancer progression.. Keywords: Gene expression profiling in two dimensional vs three dimensional cell culture

2007-12-14 | GSE9747 | GEO

Transcription profiling of human MDAMB231 breast cancer cells by Parvin-beta in 2D vs 3D culture conditions

Project description:Parvin-beta is a focal adhesion protein downregulated in human breast cancer cells. Loss of Parvin-beta contributes to increased integrin-linked kinase activity, cell-matrix adhesion, and invasion through the extracellular matrix in vitro. The effect of ectopic Parvin-beta expression on the transcriptional profile of MDA-MB-231 breast cancer cells, which normally do not express Parvin-beta was evaluated. Particular emphasis was placed upon propagating MDA-MB-231 breast cancer cells in three-dimensional culture matrices. Gene expression profiles of vector control and Parvin-beta transfected MDA-MB-231 cells cultured on (A) monomeric type I collagen coated plastic, (B) embedded in a type I collagen gel, and (C) embedded in basement membrane (growth factor reduced Matrigel), were compared. Interestingly, Parvin-beta re-expression in MDA-MB-231 cells increased the mRNA expression, serine 82 phosphorylation (mediated by CDK9), and activity of the nuclear hormone receptor, peroxisome proliferator-activated receptor gamma (PPARgamma) and a concomitant increase in lipogenic gene expression as a downstream effector of PPARgamma. Importantly, Parvin-beta suppressed breast cancer growth in vivo with associated decreased proliferation. These data suggest that Parvin-beta might influence breast cancer progression.. Experiment Overall Design: The MDA-MB-0231 transfectants were cultured for 7 days in each growth condition and total RNA isolated using Trizol reagent (Invitrogen). Genes either upregulated or downregulated in Parvin-beta transfectants versus vector control cells were compared among the 3 different growth conditions. Venn diagrams were generated using GeneSpring software and used to produce gene lists that were unique to a particular growth condition, or shared between two or all three growth conditions. The focus was primarily on gene expression alterations observed in the 3D collagen type I and 3D Matrigel conditions.

2008-06-16 | E-GEOD-9747 | biostudies-arrayexpress

Tang2019 - Pharmacology modelling of AURKB and ZAK interaction in TNBC

Project description:Aurora Kinase B and ZAK interaction model Equivalent of the stochastic model used in "Network pharmacology model predicts combined Aurora B and ZAK inhibition in MDA-MB-231 breast cancer cells" by Tang et. al. 2018. The only difference is cell division and partitioning of the components, which are available in the original model for SGNS2.

2024-09-02 | BIOMD0000000940 | BioModels

Gene expression profile in breast cancer cells

Project description:We report the gene expression patterns in MDA-MB-231 (a line selected for low metastatic ability), MDA-MB-231-1833 (its bone-tropic metastatic derivative line), MDA-MB-231p27CK-DD (a phosphomimetic cell line), MDA-MB-231-1833shp27 (p27 knockdown cell line), MDA-MB-231-1833PF1502 (PI3K inhibitor treatment). It shows that the gene expression pattern are regulated in a p27 phosphorylation-dependent manner.

2019-03-19 | GSE112445 | GEO

Exploring the mechanism of transcription factor TAF7 promoting the progression of triple-negative breast cancer

Project description:To further study the regulation of TAF7 on cells, the transcriptome sequencing on MDA MB-231 cells, MDA MB-231/shTAF7 cells, MDA 231-LM2 and MDA 231-LM2/shTAF7 cells were performed.

2025-01-20 | GSE276005 | GEO

LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [lnc231]

Project description:To discover the potential drivers of TNBC metastasis, we established an in vivo model by injecting MDA-MB-231cells into the tail veins of mice. Then, the breast tumor cells that successfully grew into metastatic lung tumors were collected and expanded in vitro, followed by re-injected into the tail veins of mice for lung metastasis. After three rounds of selection, a highly metastatic subline, MDA-MB-231-P3, was established, and more frequent micro-metastasis was detected in MDA-MB-231-P3 groups than that of MDA-MB-231 groups when the lungs of mice were stained with hematoxylin and eosin (HE). The lncRNA profiles of MDA-MB-231 or MDA-MB-231-P3 cells were analyzed by lncRNA sequencing. A total of 267 lncRNAs in MDA-MB-231-P3 cells were upregulated more than 2-fold in comparison to the MDA-MB-231 cells.

2021-11-29 | GSE163900 | GEO

Global analysis of cancer cell responses to USP9X inhibition

Project description:K-GG ubiquitin profiling of DLD-1 and MDA-MB-231 cells treated with the selective USP9X inhibitor WEHI-092 at 10 µM for 30 min, 6 h, and 24 h (and DMSO-treated control). This dataset also includes DLD-1 cells treated with FT671 (USP7 inhibitor) at 10 µM for 30 min and 6 h.Sample IDs:#1-5 Control 30 min DLD-1#6-10 FT671 30 min DLD-1#11-15 WEHI-092 30 min DLD-1#16-20 Control 360 min DLD-1#21-25 FT671 360 min DLD-1#26-30 WEHI-092 360min DLD-1#31-35 Control 30 min MDA-MB-231#36-40 WEHI-092 30 min MDA-MB-231#41-45 Control 360 min MDA-MB-231#46-50 WEHI-092 360 min MDA-MB-231#51-55 Control 24 h MDA-MB-231#56-60 WEHI-092 24 h MDA-MB-231

2026-04-09 | PXD073869 | Pride

Global analysis of cancer cell responses to USP9X inhibition

Project description:Treatment of cancer cells MDA-MB-231 and MiaPaca2 with WEHI-092 (10 uM, 24 h) or FT709 (10 uM, 24 h). Sample key of raw file in ZIP folder: #1-6 MDA-MB-231 DMSO (untreated); #13-18 MDA-MB-231 FT709; #19-24 MDA-MB-231 WEHI-092; #25-30 MiaPaca2 DMSO (untreated); #37-42 MiaPaca2 FT709; #43-48 MiaPaca2 WEHI-092.

2026-04-09 | PXD074729 | Pride

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