Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LIN28A modulates splicing and gene expression programs in breast cancer cells

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE71013 | GEO | 2015/07/27

SECONDARY ACCESSION(S): PRJNA290098

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells.

Project description: Not available

| S-EPMC4539381 | biostudies-literature

LIN28A modulates splicing and gene expression programs in breast cancer cells [RNA-Seq]

Project description:The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system. Methods: mRNA profiles from MCF-7M breast cancer cells treated with siRNA against non-targeting control (NT), LIN28, hnRNP A1, LIN28 and hnRNPA1 (LIN28A1) for 72 hrs were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped over 200 million sequence reads per sample to the human genome (build h19). Each of the four groups had two biological replicates. We developed a custom method to identify alternative splicing events and identified 111 genes with significant (FDR<0.05) differential splicing for LIN28 depleted cells compared to non-targeting siRNA control, as well as 249 and 182 genes for hnRNP A1 and LIN28A1 respectively. RNA-seq data were validated with by qRT–PCR analysis of a subset of genes. Conclusions: Results reveal that LIN28 regulates alternative splicing and steady state mRNA expression of genes implicated in aspects of breast cancer biology. Notably, cells lacking LIN28 undergo significant isoform switching of the ENAH gene, resulting in a decrease in the expression of ENAH exon 11a isoform. Expression of ENAH isoform 11a has been shown to be elevated in breast cancers that express HER2. mRNA profiles of MCF-7M cells treated with siRNA for NT control, LIN28, hnRNP A1, and LIN28 plus hnRNP A1 (A1) (LIN28A1) were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000

2015-07-27 | E-GEOD-71012 | biostudies-arrayexpress

LRH-1 governs vital transcriptional programs in endocrine sensitive and resistant breast cancer cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-02-27 | E-GEOD-54892 | biostudies-arrayexpress

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-13 | E-GEOD-47678 | biostudies-arrayexpress

LIN28A modulates splicing and gene expression programs in breast cancer cells [RIP-Seq]

Project description:The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system. Methods: mRNA-protein complexes (mRNP) lysates were prepared from MCF-7M cells and incubated with Protein-A Sepharose beads (Sigma-Aldrich) and either LIN28 (Abcam) or control normal rabbit serum IgG antibodies. LIN28 interacting mRNAs were identified by whole genome sequencing. Results: Using an optimized data analysis workflow, we mapped approximately 13 million sequence reads for LIN28-IP and CTL- IP (IgG), respectively to the to the human genome (build h19). Conclusions: mRNA were significantly bound by LIN28 if LIN28 RIP had 2.5 fold increase in normalized reads compared to IgG. We found that LIN28 was predominantly bound at coding exons and 3'UTRs, 38% & 45% respectively, in the 843 mRNAs within MCF-7M genome.

2015-07-27 | GSE71009 | GEO

LIN28A modulates splicing and gene expression programs in breast cancer cells [RNA-Seq]

2015-07-27 | GSE71012 | GEO

The identification of RBM47 binding sites and RBM47-dependent alternative splicing events in brain metastatic breast cancer cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-06-11 | E-GEOD-58381 | biostudies-arrayexpress

Mexican Patients with Breast Cancer

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-04 | E-GEOD-75685 | biostudies-arrayexpress

Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-11-22 | GSE96867 | GEO