GEO DataSets

(Submitter supplied) Whole transcriptome sequencing was performed to identify ncRNA transcriptome in two human TNBC cell lines under normoxia and hypoxia

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Purpose: The goal of the study is to compare NGS-derived transcriptome in an isogenic breast cancer progression model cell line system. By comparing the protein-coding and noncoding gene expression of normal versus tumorigenic breast cancer cell lines, we will be able to identify genes that show aberrant expression during breast cancer progression. Methods: We isolated poly A + RNA from four isogenic mammary epithelial cell lines showing various stages of breast cancer progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT

(Submitter supplied) To examine the role of long non-coding RNA TMPO-AS1 in breast cancer, MDA-MB-231 cells were treated with siRNAs targeting TMPO-AS1 (siTMPO-AS1) or control siRNA (siControl). 3 samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

3 Samples

Download data: CEL, CHP

(Submitter supplied) RAB11B-AS1 is induced by hypoxia and controls gene expression in breast cancer cells under hypoxia

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We used microarray to indentify KMO-regulated genes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL570

19 Samples

Download data: BED, BW, CEL

(Submitter supplied) During cancer progression, carcinoma cells encounter a variety of cytotoxic stresses such as hypoxia, nutrient deprivation, and low pH as a result of inadequate vascularization. To maintain survival and growth in the face of these physiologic stressors, a set of adaptive response pathways are induced. One adaptive pathway well studied in other contexts is the unfolded protein response (UPR), of which XBP1 is an important component. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) We report the application of ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing, to map genome-wide XBP1 binding sites in different breast cancer cell lines. We showed that HIF1α motif was enriched in XBP1 binding sites in triple negative breast cancer (TNBC) cell lines, but not enriched in ER positive breast cancer cell line. We also demonstrated that different breast cancer cell lines of the same sub-type had similar XBP1 binding sites, whereas different breast cancer sub-types had majorly different XBP1 binding sites. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: BED, BW

(Submitter supplied) MAFK is one of small Maf transcripton factor famiy molecules. We found MAFK is highly expressed in several cancer cells and related to tumorigenesis. Then, we established MAFK stable cell lines using NMuMG cells (mouse mammary glad epithelium) and used microarrays to examine gene expression alteration.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

3 Samples

Download data: CEL

(Submitter supplied) To develop and validate novel multigene signatures to facilitate individualized treatment of TNBC patients By integrating expression profiles of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

198 Samples

Download data: CEL

(Submitter supplied) By using shRNAs the lnc-klhdc7b was silenced in the cell line HCC1187, the shRNA-1 carried a ~75% silencing compared to the negative control (NC). We evaluated the role of LncKLHDC7B on oncogenic phenotypes in the IM breast cancer HCC1187 cell line model. The knockdown of LncKLHDC7B was achieved with ~75% of silencing efficiency. A complete genomic analysis of the transcriptomic state after silencing of LncKLHDC7B revealed an impact on the global expression of transcripts

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

6 Samples

Download data: CEL, CHP

(Submitter supplied) The ubiquitous nature of lncRNAs to comprehensively alter cellular transcriptional networks led us to hypothesize that BORG is capable of compelling metastasic, chemoresistant, and pro-survival activities in triple-negative breast cancers by inducing global transcriptomic reprogramming. As such, we performed RNA-seq to garner mechanistic insights into BORG-dependent pathways within D2.OR cells. Accordingly, transcriptional profiles associated with aggressive breast cancers and adaptive survival programs were amongst the top enriched pathways in BORG-expressing D2.OR cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: XLSX

(Submitter supplied) To interrogate the molecule changes induced by hypoxia in differentiated T cells, T cells from three donors cultured in normoxia and hypoxia conditions were subject to RNA-seq analysis

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV