Similar Datasets
Project description:Clariom D expression in breast cancer samples
| PRJNA524163 | ENA
Project description:Experiment description to give context to the data set: Ductal carcinoma in situ (DCIS), the most common type of pre-invasive lesion of breast, is being detected with increasing frequency with the advent of mammographic screening. Surgery is the mainstay for the treatment of DCIS. Based on the clinic-pathological features of DCIS, this may be followed by radiotherapy and/or endocrine therapy. The qualitative assessment of histological grade, expression of single protein biomarkers and more recently, mRNA analysis (DCIS Score) have been used to make these decisions. However, these factors do not fully predict the likelihood of development of invasive breast cancer treated with breast-conserving surgery. A majority of women with ductal carcinoma in situ (DCIS) receive breast-conserving surgery (BCS) but then face a risk of development of invasive breast cancer. Using Human Clariom D Pico Assay, we aim to compare the transcriptome profiles of DCIS in relation to development of invasive breast cancer (INV-BC) versus Non-INV-BC cases. Experimental Methods Clariom D Pico Human Transcriptome Array were performed according to Applied Biosystems/Thermo Fisher Scientific’s instructions. Experimental protocols are summarized in detail in Supplementary Methods (Supplementary Data). Sample annotation We compared the relative gene expression in development of invasive breast cancer (INV-BC) versus Non-INV-BC cases in Singapore cohort-59 cases (discovery cohort) and Italian cohort-50 cases (validation cohort). Microplate Plate and Well IDs are also provided as Clariom D ID list per cohort. Author information Dr. Sunil Badve is the Principal Investigator. Raw Data Probe Cell Intensity (CELL) and .ARR files which contain the design information for this study are provided (Human Clariom D Pico Assay).
2022-06-02 | E-MTAB-9856 | biostudies-arrayexpress
Project description:RNA was isolated from FFPE tissue sections and expression profile of miRNAs determined by hybridization to Affymetrix GeneChip miRNA 4.0 Array Both normal and cancer samples were used. Normal cases included cosmetic reduction mammoplasties (the only true normal tissue) and tissues with some morphological abnormalities. Some benign, non-cancer, cases were also included. Breast cancer cases included invaive ductal and lobullar carcinomas as well as metaplastic breast cancer
2023-01-30 | GSE144534 | GEO
Project description:Clariom D gene array of HBMEC cells
| PRJNA991457 | ENA
Project description:A transcriptome signature which discriminate efficiently primary and radiation induced breast angiosarcomas can be generated from FFPE tumor samples.FFPE samples are good material to unlock relevant informations from tumors. The transcriptome of 35 FFPE breast angiosarcomas (10 primary and 25 radiation induced) were analysed using Affymetrix Human Exon 1.0 ST arrays according to the FFPE dedicated protocole from NuGEN and compared to paired fresh frozen samples previously analysed. FF Samples are also available in Array Express as E-MEXP-3252.
2016-08-08 | E-GEOD-49790 | biostudies-arrayexpress
Project description:We implemented an optimized processing, using alternative Chip Description Files (CDFs) and fRMA normalization, which improve the quality of downstream analysis. We profiled 44 FFPE primary breast cancer samples using Affymetrix HG-U133 Plus 2.0 microarray platform after RNA amplification with the Nugen WT-Ovation FFPE System
2014-02-01 | E-GEOD-38554 | biostudies-arrayexpress
Project description:Clariom D gene array of Bone Marrow derived macrophages
| PRJNA1113971 | ENA
Project description:Expression and differential expression analysis of breast cancer patient samples and normal samples from breast reduction operations. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Breast tissue samples from breast reduction operations were provided from the Colosseum Clinic, Oslo in co-operation with Akershus University Hospital, Lørenskog and are referred to as normal tissue. Expression and differential expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.
2015-01-23 | GSE50428 | GEO
Project description:The use of Affymetrix U133 2.0 Plus chips on FFPE samples when coupled with a qPCR-based sample pre-assessment step, yielded satisfactory results from the point of view of biological reliability. When compared with the Illumina DASL WG platform, specifically designed for degraded RNA, the data generated with the Affymetrix platform showed a wider interquartile range (1.32 vs 0.57, p<2.2x10-16) suggesting a superior discriminatory power within samples as indicated by the good agreement with the immunohistiochemically derived ER status. FFPE primary breast cancer samples profiled using Illumina DASL WG platform after RNA amplification with the Nugen WT-Ovation FFPE System
2015-02-25 | GSE51451 | GEO
Project description:The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. Compared to FNA specimens, FFPE samples yielded relatively more degraded RNA, and 80% of the samples deemed suitable for cDNA-mediated annealing, selection, extension and ligation (DASL) assay. It is able to demonstrate that gene profiles from FFPE microarrays were reproducible and correlated well with the corresponding gene profiles from FNA microarrays. The gene profiles from both FNA and FFPE could differentiate the four breast cancer subtypes, and the expression levels of corresponding gene set were consistent with qRT-PCR and correlated to the clinical outcomes on published microarray data. It supports the use of FFPE specimens to develop a prognostic tool for breast cancers which can obviate the need for fresh specimens.
2011-06-22 | GSE23385 | GEO