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Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells

ABSTRACT: We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity.

ORGANISM(S): Homo sapiens

PROVIDER: GSE49608 | GEO | 2014/07/24

SECONDARY ACCESSION(S): PRJNA214464

REPOSITORIES: GEO

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Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells

Project description:We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity. Cells were pulsed with 4-thiouridine for 2 hours and then RNA was extracted at 0, 2, 4, and 7 hr time-points in quadruplicate from each cell line. 4sU labeling followed by RNA-seq was then used to measure the abundance of transcripts in each population. A decay rate was estimated based on the rate at which transcript abundance was reduced at these time-points.

2014-07-24 | E-GEOD-49608 | biostudies-arrayexpress

RNA sequencing of MDA-LM2 and MDA-Parental cells

Project description:We used RNA sequencing to compare MDA-MB-231 cells to their higly metastatic MDA-LM2 derivatvies.

2021-03-30 | GSE160953 | GEO

Regulatory consequences of SOX4 knock-down in MDA-LM2 cell line

Project description:Transcriptomic profiling of SOX4 knock-down MDA-LM2 cell line resulted in down-regulation of its transcriptional target gene, TMEM2. Two independent siRNAs were used to knock down SOX4 in metastatic MDA-LM2 cells. The cells were then subjected to transcripome profiling in comparison to control siRNA-transfected cells.

2016-03-15 | E-GEOD-79202 | biostudies-arrayexpress

Analysis of HNRNPC Interactome in MDA-MB231 parental and LM2 cells

Project description:To define and compare the interactomes of the RNA binding protein HNRNPC in poorly vs. efficiently metastatic breast adenocarcinoma cells, we carried out immunoprecipitation of endogenous HNRNPC from parental MDA-MB231 cells vs. its highly metastatic isogenic derivate, the MDA-MB231-LM2 cells. We used a non-specific MOUSE IgG IP from each line as control. Each IP was performed in triplicate, and analysed by LC-MS/MS, on a Thermo Q-Exactive-plus instrument.

2023-02-19 | PXD029560 | Pride

SRSF1 HITS-CLIP in MDA-LM2

Project description:To identify SRSF1 binding sites on RNAs, we performed HITS-CLIP of endogenous SRSF1 in MDA-LM2 cells

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Gene expression profilling of poorly metastatic MDA cells and highly metastatic LM2 cells.

Project description:Comparison of gene expression between the breast cancer cell line MDA-MB-231 and its highly metastatic deriviate LM2 cells (described in Minn et al., Nature 2005). Results hilghlights potential metastasis promoting and suppressing genes.

2011-12-16 | GSE23904 | GEO

Gene expression profilling of poorly metastatic MDA cells and highly metastatic LM2 cells.

2011-12-16 | E-GEOD-23904 | biostudies-arrayexpress

Regulatory consequences of TARBP2 knock-down in MDA-LM2 cell-line

Project description:siRNA-mediated knock-down followed by transcriptomic profiling revealed that silencing of TARBP2 resulted in a significant up-regulation of sRSE-carrying transcripts. Two independent siRNAs were used to knock down TARBP2 in metastatic MDA-LM2 cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.

2014-07-24 | E-GEOD-49611 | biostudies-arrayexpress

Regulatory consequences of TARBP2 knock-down in MDA-LM2-shDicer cell-line

Project description:siRNA-mediated knock-down followed by transcriptomic profiling revealed that silencing of TARBP2 resulted in a significant up-regulation of sRSE-carrying transcripts. Two independent siRNAs were used to knock down TARBP2 in metastatic MDA-LM2 shDicer cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.

2014-07-24 | E-GEOD-56950 | biostudies-arrayexpress

Regulatory consequences of TARBP2 knock-down in MDA-LM2 cell-line [stability experiment]

Project description:siRNA-mediated knock-down followed by transcriptomic profiling revealed that silencing of TARBP2 resulted in a significant increase in the stability of sRSE-carrying transcripts. Two independent siRNAs were used to knock down TARBP2 in metastatic MDA-LM2 cells. The cells were then subjected to whole-genome transcript stabiliy measurements in comparison to mock-transfected cells.

2014-07-24 | E-GEOD-49612 | biostudies-arrayexpress

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