Similar studies for GEO DataSets (Select 200038790) - GEO DataSets

Select item 2000387901.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [DGE]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL14761
10 Samples

Download data: TXT

Series

Accession:: GSE38790

ID:: 200038790

PubMed Similar studies SRA Run Selector

Select item 2000691142.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [RNA-Seq]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
10 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE69114

ID:: 200069114

Select item 2000691123.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 3]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL18573
23 Samples

Download data: BW

Series

Accession:: GSE69112

ID:: 200069112

PubMed Similar studies SRA Run Selector

Select item 2000676194.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [methylation450]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
20 Samples

Download data: TXT

Series

Accession:: GSE67619

ID:: 200067619

Select item 2000394125.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [SNP]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Genome variation profiling by SNP array

Platform:: GPL6801
19 Samples

Download data: CEL, XLSX

Series

Accession:: GSE39412

ID:: 200039412

PubMed Similar studies

Select item 2000387916.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [methylation27]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL8490
9 Samples

Download data: TXT

Series

Accession:: GSE38791

ID:: 200038791

Select item 2000387897.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 2]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL13393
9 Samples

Download data: BED, PROBSCOREISLAND

Series

Accession:: GSE38789

ID:: 200038789

PubMed Similar studies SRA Run Selector

Select item 2000387888.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 1]

(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9052
6 Samples

Download data: BED

Series

Accession:: GSE38788

ID:: 200038788

PubMed Similar studies SRA Run Selector

Select item 2000385489.

Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by array; Genome variation profiling by SNP array; Methylation profiling by genome tiling array

7 related Platforms
106 Samples

Download data: BED, BW, CEL, FPKM_TRACKING, PROBSCOREISLAND, TXT

Series

Accession:: GSE38548

ID:: 200038548

Select item 20002530710.

The retinoblastoma gene is targeted for rearrangements in BRCA1-deficient basal-like breast cancer.

(Submitter supplied) Breast tumors from BRCA1 germ line mutation carriers typically exhibit features of the basal-like molecular subtype. However, the specific genes recurrently mutated as a consequence of BRCA1 dysfunction have not been fully elucidated. In this study, we utilized gene expression profiling to molecularly subtype 577 breast tumors, including 73 breast tumors from BRCA1/2 mutation carriers. Focusing on the RB1 locus, we analyzed 33 BRCA1-mutated, 36 BRCA2-mutated and 48 non-BRCA1/2-mutated breast tumors using a custom-designed high-density oligomicroarray covering the RB1 gene. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL5345
577 Samples

Download data: GPR, TXT

Series

Accession:: GSE25307

ID:: 200025307

Select item 20001917711.

Subtypes of familial breast tumors revealed by expression and copy number profiling

(Submitter supplied) We analysed a cohort of 75 BRCA1, BRCA2 and non-BRCA1/2 breast tumors by gene expression profiling and found that 74% BRCA1 tumors were basal-like, 73% of BRCA2 tumors were luminal A or B, and 52% non-BRCA1/2 tumors were luminal A. Thirty-four tumors were also analysed by single nucleotide polymorphism-comparative genomic hybridization (SNP-CGH) arrays. Copy number data could predict whether a tumor was basal-like or luminal with high accuracy, but could not predict its mutation class. more...

Organism:: Homo sapiens

Type:: Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:: GPL6986 GPL6106
109 Samples

Download data: TXT

Series

Accession:: GSE19177

ID:: 200019177

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002641112.

Interactions with Fibroblasts are Distinct in Basal-like and Luminal Breast Cancers

(Submitter supplied) Basal-like breast cancers have several well-characterized distinguishing molecular features, but most of these are features of the cancer cells themselves. The unique stromal-epithelial interactions, and more generally, microenvironmental features of basal-like breast cancers, have not been well characterized. To identify characteristic microenvironment features of basal-like breast cancer, we performed cocultures of several basal-like breast cancer cell lines with fibroblasts (reduction mammoplasty-derived fibroblast line; RMF) and compared these to cocultures of luminal breast cancer cell lines with fibroblasts. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platforms:: GPL8269 GPL4133
99 Samples

Download data

Series

Accession:: GSE26411

ID:: 200026411

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001679513.

Affymetrix HG-U133A gene expression profiles of 39 human breast cancer cell lines

(Submitter supplied) Microarrays were used to detail the global programme of gene expression underlying breast cancer cell lines. We identified two main groups of luminal-type and basal-type breast cancer cell lines by unsupervised Pearson correlation of breast cancer cell lines and intrinsic subtyping. Supervised analysis on spindle versus non-spindle breast cancer cell lines identified a spindle cell signature of 1,144 genes identifying all spindle, basal-type, E-cadherin methylated breast cancer cell lines.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL96
39 Samples

Download data: CEL

Series

Accession:: GSE16795

ID:: 200016795

Select item 20019659514.

Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
56 Samples

Download data

Series

Accession:: GSE196595

ID:: 200196595

PubMed Full text in PMC Similar studies

Select item 20019659415.

Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks [siZBED2_siFOXA1]

(Submitter supplied) RNA-seq Series of bladder carcinoma cell lines RT112 and SCaBER treated by siZBED2 and FOXA1.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
24 Samples

Download data: CSV, TXT, XLSX

Series

Accession:: GSE196594

ID:: 200196594

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20019659316.

Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks [CrispR_FOXA1]

(Submitter supplied) RNA-seq Series of Bladder carcinoma cell lines RT112 and SD48 mutated for FOXA1 by CrispR.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
16 Samples

Download data: CSV, TXT, XLSX

Series

Accession:: GSE196593

ID:: 200196593

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20019657917.

Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks [siFOXA1]

(Submitter supplied) RNA-seq Series of bladder carcinoma cell lines RT112 and SCaBER treated by siFOXA1.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
16 Samples

Download data: CSV, TXT, XLSX

Series

Accession:: GSE196579

ID:: 200196579

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20019560818.

RNA-seq Series of Bladder carcinoma Cell lines associated with the Study "Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks"

(Submitter supplied) Background: Muscle-invasive bladder cancer is a common aggressive disease with unmet clinical needs. Recent work established a set of consensus bladder cancer transcriptomic subtypes that distinguishes the cell identity of bladder cancers for improved diagnosis and treatment. However, how these distinct subtypes are regulated remains unclear. Given the link between super-enhancers and the regulation of cell identity, we hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of the various bladder cancer subtypes. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
8 Samples

Download data: CSV, TXT

Series

Accession:: GSE195608

ID:: 200195608

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20019388919.

Establishing the enhancers/super-enhancers landscape and associated alterations leading to bladder cancer

(Submitter supplied) Provide a first characterization of the chromatin landscapes of bladder cancers. Using ChIPseq (H3K27ac, H3K27me3, H3K9me3) in tumors characterized at the genetic, DNA methylation and transcriptomic levels, we will identify active regulatory regions. We will in particular define the super-enhancers active in the different molecular subtypes recently described.