GEO DataSets

(Submitter supplied) Women with germline mtuation in BRCA1 have increased risk for developing hereditary breast cancer. The role of the epitheilum-assocaited niche during BRCA1-driven tumor intiation remains unclear. Here, we show that the pre-malignant stromal niche promotes epithelial prolifeation and BRCA1-driven cancer intiation in trans. Using single-cell RNA seq analysis of human pre-neoplastic BRCA1 and control breast tissue, we show that stromal cells provide numerous pro-proliferative paracrine signals inducing epithelial proliferation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

22 Samples

Download data: TXT

(Submitter supplied) RANK-positive and RANK-negative luminal progenitor cells were isolated by FACS from histologically normal human breast tissue from wild-type human donors. RNA-seq gene expression profiling was used to find differentially expressed genes between the RANK-positive and RANK-negative cell populations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) BRCA1 functions in multiple biological processes, including double-strand break repair, replication stress suppression, transcriptional regulation, and chromatin reorganization. While non-malignant cells carrying cancer-predisposing BRCA1 mutations exhibit increased genomic instability, it remains unclear whether BRCA1 haploinsufficiency affects transcription and chromatin dynamics. Here we show that primary mammary epithelial cells from women with BRCA1 mutations (BRCA1mut/+) display significant loss of H3K27ac-associated super-enhancers.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21290

6 Samples

Download data: BED

(Submitter supplied) Mammary organoids treated with a 28 day menstrual cycle profile of estradiol and progesterone with or without TPA: Comparison of normal versus BRCA1 mut cells. Purpose: The goals of this study are to determine 1) the effects of a 28 day menstrual cycle profile of estradiol and progesterone, 2) the effects of TPA, and 3) the responses in normal versus BRCA1 carriers, in benign breast organoids using RNA-seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: TXT

(Submitter supplied) Gene expression profiles of normal human mammary tissue from BRCA1 mutation carriers, non-BRCA1/2 mutation carriers and normal women. RNA was prepared from normal breast tissue (confirmed by pathology) from reduction mammoplasties (n=5) and prophylactic mastectomies of known BRCA1 (n=7) and non-BRCA1/2 mutation carriers (n=8). non-BRCA1/2 carriers were individuals with a strong family history of breast cancer (kConFab Category 1 (http://www.kconfab.org/Collection/Eligibility.shtml) where no mutation in BRCA1 or BRCA2 has been identified in the family by high sensitivity testing (http://www.kconfab.org/Progress/Sensitivity.shtml) of any individual affected by breast or ovarian cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

20 Samples

Download data: TXT

(Submitter supplied) To delineate epithelial subpopulations in human mammary tissue, hematopoietic and endothelial cells were depleted from freshly isolated cell suspensions derived from reduction mammoplasties by fluorescence-activated cell sorting. The resultant Lin- population was fractionated into four distinct subpopulations using CD49f (α6-integrin) and epithelial cell adhesion molecule (EpCAM; also referred to as CD326 and ESA). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

12 Samples

Download data: TXT

(Submitter supplied) Goal of this study is to develop the single cell map of breast tissues of women who carry germline mutations in BRCA1 or BRCA2 genes. Towards this goal, we performed single cell RNA sequencing (sc-RNAseq) of cells isolated from cryopreserved tissues.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: H5

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21273

517 Samples

Download data

(Submitter supplied) The mammary epithelia are mainly composed of two distinct lineages, the basal and luminal cells. In our MMTV-Cre; Brca1flox/flox mouse model, we found the Brca1 knockout mainly occurred in the luminal cells, which will lead the mammary tumorigenesis. To investigate the Brca1 deficiency mediated mammary tumorigenesis, we sorted the luminal cells from wild type mice and MMTV-Cre; Brca1flox/flox mice for RNAseq analysis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: TXT

(Submitter supplied) Brca1 mutation predisposes women to early onset of breast and ovarian cancers.Through its diverse functions in DNA damage repair, cell cycle control, transcription regulation, ubiquitination and so on, BRCA1 acts as a very significant tumor suppressor and genomic safeguard. Brca1 deficiency induces severe cellular stress, when occurring in the mammary glands, it impairs the regular developmental process and eventually causes tumorigenesis due to accumulation of genome instability and other mechanisms. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

477 Samples

Download data: TXT

(Submitter supplied) Brca1 mutation predisposes women to early onset of breast and ovarian cancers.Through its diverse functions in DNA damage repair, cell cycle control, transcription regulation, ubiquitination and so on, BRCA1 acts as a very significant tumor suppressor and genomic safeguard. Brca1 deficiency induces severe cellular stress, when occurring in the mammary glands, it impairs the regular developmental process and eventually causes tumorigenesis due to accumulation of genome instability and other mechanisms. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

12 Samples

Download data: CSV

(Submitter supplied) Brca1 mutation predisposes women to early onset of breast and ovarian cancers.Through its diverse functions in DNA damage repair, cell cycle control, transcription regulation, ubiquitination and so on, BRCA1 acts as a very significant tumor suppressor and genomic safeguard. Brca1 deficiency induces severe cellular stress, when occurring in the mammary glands, it impairs the regular developmental process and eventually causes tumorigenesis due to accumulation of genome instability and other mechanisms. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21273 GPL17021

23 Samples

Download data: TXT

(Submitter supplied) We generate induced pluripotent stem cells (iPSCs) from healthy individuals and young ovarian cancer patients with germline pathogenic BRCA1 mutations. We then differentiate them into a human iPSC-derived fallopian tube organoid model. We recapitulated BRCA1 mutant ovarian carcinogenesis in vitro and showed tumors in vivo. Using the IPSC derived fallopian tube organoid model, we identify a unique transcriptional profile associated with BRCA1 mutation similar to the ovarian cancer profile.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) The transcriptional profile of WapCre;Rank;Brca1;p53 and WapCre;Brca1;p53 mouse primary mammary tumor cells was determined by mRNA sequencing and uncovered differences in their molecular signatures including genes involved in oncogenesis, basic metabolism, RNA metabolism, or the regulation of mammary stem cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) In order to investigate the mechanisms underlying defective alveologenesis caused by RANK over-expression in mice, global gene expression profiles from primary acinar cultures of mammary epithelial cells were analyzed.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2872

72 Samples

Download data: TXT

(Submitter supplied) BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

46 Samples

Download data: BW

(Submitter supplied) Most BRCA1-associated breast tumors are basal-like yet originate from luminal progenitor cells. BRCA1 is best known for its functions in DNA repair and resolution of DNA replication stress. However, it is unclear whether loss of these ubiquitously important functions of BRCA1 fully explains the cell lineage-specific increase in breast tumor development. Cell culture-based studies implicate BRCA1 in elimination of R-loops, DNA-RNA hybrid structures involved in transcriptional regulation and genetic instability. more...

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: BED

(Submitter supplied) BRCA1 molecule, known to be implicated in DNA repair and its alterations were associated to familial breast cancer prediposition. Genome of the patients with familial breast cancer predispostion harbor some germinal alterations in BRCA1 locus. Cells from peripheral blood of human with haplodeficiency BRCA1 locus and also from comparative sample (BRCA1 unaffected) were collected to produce induced pluripotent stem cell by classical protocol (Yamanaka OKSM) and Sendai Stem cell reprogammation which was validated by expression assessment of pluripotent stem cell markers and induction of teratoma after xenotransplantation mice model. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

4 Samples

Download data: CEL

(Submitter supplied) BRCA1 mutation-carriers are predisposed to develop Basal-like breast cancer (BLBC), and p53 mutations are present in the majority of human BLBC cases, suggesting loss of these two tumor suppressors play key roles in development of BLBC. Recent studies suggest that the majority of human breast cancers, including BLBC, may originate from mammary epithelial cells (MECs) in the luminal lineage. However, how loss of p53 and BRCA1 contributes to development of BLBC from luminal MECs remains largely elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

4 Samples

Download data: MTX, TSV

(Submitter supplied) BRCA1 mutation-carriers are predisposed to develop Basal-like breast cancer (BLBC), and p53 mutations are present in the majority of human BLBC cases, suggesting loss of these two tumor suppressors play key roles in development of BLBC. Recent studies suggest that the majority of human breast cancers, including BLBC, may originate from mammary epithelial cells (MECs) in the luminal lineage. However, how loss of p53 and BRCA1 contributes to development of BLBC from luminal MECs remains largely elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: TXT