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Series GSE96860 Query DataSets for GSE96860
Status Public on Nov 22, 2017
Title Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif p-values, and enrichment of H3K4me1 and H3KK27. When applied across the 13 different breast cancer cell lines, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype specific transcription factors that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes.
 
Overall design To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer.
 
Contributor(s) Franco HL, Nagari A, Malladi V, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SY, Kraus WL
Citation(s) 29273624, 29458327
Submission date Mar 21, 2017
Last update date May 15, 2019
Contact name W. Lee Kraus
E-mail(s) lee.kraus@utsouthwestern.edu
Organization name UT Southwestern Medical Center
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-8511
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (52)
GSM2545221 76NF2V rep1 (RNA-Seq)
GSM2545222 76NF2V rep2 (RNA-Seq)
GSM2545223 76NF2V rep3 (RNA-Seq)
This SubSeries is part of SuperSeries:
GSE96867 Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis
Relations
BioProject PRJNA379957
SRA SRP102239

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Supplementary file Size Download File type/resource
GSE96860_76NF2V_RNAseq_Untreated_MinusStrand.bw 37.8 Mb (ftp)(http) BW
GSE96860_76NF2V_RNAseq_Untreated_PlusStrand.bw 38.2 Mb (ftp)(http) BW
GSE96860_AU565_RNAseq_Untreated_MinusStrand.bw 37.5 Mb (ftp)(http) BW
GSE96860_AU565_RNAseq_Untreated_PlusStrand.bw 37.8 Mb (ftp)(http) BW
GSE96860_HCC1937_RNAseq_Untreated_MinusStrand.bw 37.6 Mb (ftp)(http) BW
GSE96860_HCC1937_RNAseq_Untreated_PlusStrand.bw 38.1 Mb (ftp)(http) BW
GSE96860_HCC1954_RNAseq_Untreated_MinusStrand.bw 37.8 Mb (ftp)(http) BW
GSE96860_HCC1954_RNAseq_Untreated_PlusStrand.bw 37.9 Mb (ftp)(http) BW
GSE96860_MB231_RNAseq_Untreated_MinusStrand.bw 37.8 Mb (ftp)(http) BW
GSE96860_MB231_RNAseq_Untreated_PlusStrand.bw 38.2 Mb (ftp)(http) BW
GSE96860_MB361_RNAseq_Untreated_MinusStrand.bw 38.7 Mb (ftp)(http) BW
GSE96860_MB361_RNAseq_Untreated_PlusStrand.bw 38.8 Mb (ftp)(http) BW
GSE96860_MB436_RNAseq_Untreated_MinusStrand.bw 38.1 Mb (ftp)(http) BW
GSE96860_MB436_RNAseq_Untreated_PlusStrand.bw 38.5 Mb (ftp)(http) BW
GSE96860_MB468_RNAseq_Untreated_MinusStrand.bw 38.5 Mb (ftp)(http) BW
GSE96860_MB468_RNAseq_Untreated_PlusStrand.bw 38.9 Mb (ftp)(http) BW
GSE96860_MCF10A_RNAseq_Untreated_MinusStrand.bw 37.9 Mb (ftp)(http) BW
GSE96860_MCF10A_RNAseq_Untreated_PlusStrand.bw 38.3 Mb (ftp)(http) BW
GSE96860_MCF7_RNAseq_Untreated_MinusStrand.bw 37.2 Mb (ftp)(http) BW
GSE96860_MCF7_RNAseq_Untreated_PlusStrand.bw 37.6 Mb (ftp)(http) BW
GSE96860_SKBR3_RNAseq_Untreated_MinusStrand.bw 37.8 Mb (ftp)(http) BW
GSE96860_SKBR3_RNAseq_Untreated_PlusStrand.bw 37.9 Mb (ftp)(http) BW
GSE96860_UACC812_RNAseq_Untreated_MinusStrand.bw 38.3 Mb (ftp)(http) BW
GSE96860_UACC812_RNAseq_Untreated_PlusStrand.bw 38.4 Mb (ftp)(http) BW
GSE96860_ZR751_RNAseq_Untreated_MinusStrand.bw 37.9 Mb (ftp)(http) BW
GSE96860_ZR751_RNAseq_Untreated_PlusStrand.bw 38.3 Mb (ftp)(http) BW
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