Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA177029 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We profiled basal gene expressed levels of 21 cell lines (18 cancer and 3 non-tumorigenic) using Affymetrix HG-U133_plus2 GeneChip microarrays. Goal of the experiment was to benchmark a number of algorithms for biomarker detection all of which utilize gene expression data.
2012-10-10 | GSE41445 | GEO
Project description:We profiled basal gene expressed levels of 21 cell lines (18 cancer and 3 non-tumorigenic) using Affymetrix HG-U133_plus2 GeneChip microarrays. Goal of the experiment was to benchmark a number of algorithms for biomarker detection all of which utilize gene expression data. Cell lines were cultivated in appropriate media according to supplier recommendations. Goal was to acquire a basal gene expression profile of 21 common cell lines.
2012-10-10 | E-GEOD-41445 | biostudies-arrayexpress
Project description:RNA-seq profiling of human non-tumorigenic and cancer breast cell lines
| PRJNA767228 | ENA
Project description:We have generated tumorigenic (S2N) and non-tumorigenic (S2), normal-like to basal-like breast cancer cell lines from primary tumors. At high in vivo inoculation cell numbers of 10^6 cells/mouse both S2N and S2 monolayer as well as sphere culture cells grew at similar rates. However, at low inoculation cell numbers down to 10^3 cells only S2N sphere cells generated xenograft tumors. mRNA profiling revealed a unique cluster pattern of the tumorigenic S2N sphere cells, but a detailed analysis of TIC relevant transcription factors like Oct3, Sox and Nanog family members, Myc, Slug or Twist1 revealed no consistently increased expression in the highly tumorigenic cell lines. Our data indicate that the intrinsic genetic and functional markers investigated are not solely indicative of the in vivo tumorigenicity of putative breast tumor-initiating cells. 4 samples with 3 replicates each
2012-12-21 | E-GEOD-32526 | biostudies-arrayexpress
Project description:Expression data from Non small cell lung cancer cell lines
| PRJNA111915 | ENA
Project description:Increased proliferation and elevated levels of protein synthesis are characteristic of transformed and tumor cells. Though components of the translation machinery are often misregulated in cancers, how tRNA plays a role in cancer cells has not been explored. We compare genome-wide tRNA expression in tumorigenic versus non-tumorigenic breast cell lines, as well as tRNA expression in breast tumors versus normal breast tissues. In tumorigenic versus non-tumorigenic cell lines, nuclear-encoded tRNAs increase by up to 3-fold and mitochondrial-encoded tRNAs increase by up to 5-fold. In tumors versus normal breast tissues, both nuclear and mitochondrial-encoded tRNAs increase by up to 10-fold. This tRNA over-expression is selective and coordinates with the properties of cognate amino acids. Nuclear- and mitochondrial-encoded tRNAs exhibit distinct expression patterns, indicating that tRNAs can be used as biomarkers for breast cancer. We analyzed tRNA expression levels in 2 non-tumorigenic breast cell lines, 6 tumorigenic breast cancer cell lines, 3 normal breast tissue samples, and 9 breast tumor samples. We used a non-tumorigenic breast cell line (MCF10A) as a reference sample in all hybridizations. All data is dye-swapped.
2010-05-22 | E-GEOD-17945 | biostudies-arrayexpress
Project description:We have generated tumorigenic (S2N) and non-tumorigenic (S2), normal-like to basal-like breast cancer cell lines from primary tumors. At high in vivo inoculation cell numbers of 10^6 cells/mouse both S2N and S2 monolayer as well as sphere culture cells grew at similar rates. However, at low inoculation cell numbers down to 10^3 cells only S2N sphere cells generated xenograft tumors. mRNA profiling revealed a unique cluster pattern of the tumorigenic S2N sphere cells, but a detailed analysis of TIC relevant transcription factors like Oct3, Sox and Nanog family members, Myc, Slug or Twist1 revealed no consistently increased expression in the highly tumorigenic cell lines. Our data indicate that the intrinsic genetic and functional markers investigated are not solely indicative of the in vivo tumorigenicity of putative breast tumor-initiating cells.
2012-12-21 | GSE32526 | GEO
Project description:We performed quantitative TMT-based proteomic analysis of eight human-derived breast cell lines growing in 2D. The dataset includes the total and phospho-proteomes of seven tumour cell lines: T47D (Epithelial, Luminal, ER+/PR+/HER2-), BT474 (Epithelial, Luminal, ER+/PR+/HER2+), SKBR3 (Epithelial, Luminal, ER-/PR-/HER2+), MDA-MB-468 (Epithelial, Basal A, ER-/PR-/HER2-), MDA-MB-231 (Mesenchymal, Basal B, ER-/PR-/HER2-), MDA-MB-231-LM2 (Mesenchymal, Basal B, ER-/PR-/HER2-, a highly metastatic subpopulation 4175 from MDA-MB-231), and SUM159 (Mesenchymal, Basal B, ER-/PR-/HER2-) and one non-tumour cell line: MCF10A (Epithelial, Basal B, ER-/PR-/HER2-). We achieved a depth of over 8,000 proteins and a total of over 20,000 phosphopeptides with MS2 acquisition covering a wide range of biological processes. These eight lines encompass a wide range of genetic subtypes and have diverse morphologies in either 2D (epithelial vs mesenchymal), and/or in 3D environments (Mass, Grape-like, Stellate, Round) (Neve RM, 2006) (Kenny PA, 2007). The study also explored the effects of TGF-β1 during 10 days on the non-tumorigenic MCF10A cells, and their posterior washout and recovery for 40 days. TGF-β1 is a cytokine known to induce epithelial-to-mesenchymal transition (EMT), a process associated with cancer progression (Xu J, 2009) (Nieto, 2016). The data can be analysed in isolation or in combination with other orthogonal datasets such as transcriptomes or image-based data (OMICS), for the purpose of predicting tumour outcome, identifying markers, drug response or mechanisms of resistance to therapeutics. These data can provide insights for therapeutic strategies and better understanding of the diverse molecular landscapes of breast cancer cells.
2024-09-16 | PXD047164 | Pride
Project description:Basal gene expression of breast cancer cell lines
| PRJNA133599 | ENA
Project description:MicroRNAs (miRNAs), a class of short non-coding RNAs, often act post-transcriptionally to inhibit gene expression. We used a bead-based flow cytometric profiling method to obtain miRNA expression data for 93 primary human breast tumours, 21 cell lines and five normal breast samples. Of 309 human miRNAs assayed we identify 133 miRNAs expressed in human breast and breast tumours. We used mRNA expression profiling to classify the breast tumours into Luminal A, Luminal B, Basal-like, HER2+/ER- and Normal-like. A number of miRNAs are differentially expressed between these molecular tumour subtypes and individual miRNAs are associated with clinicopathological factors. Furthermore, we find that miRNAs could classify basal versus luminal tumour subtypes in an independent data set. Keywords = miRNA Keywords = microRNA Keywords = normal Keywords = tumour Keywords = cell line Keywords = breast Keywords = cancer Keywords: Bead-based flow cytometric profiling miRNA expression data for 93 primary human breast tumours, 21 cell lines and five normal breast samples
2007-10-09 | E-GEOD-7842 | biostudies-arrayexpress