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Sample GSM1219109 Query DataSets for GSM1219109
Status Public on Jan 23, 2015
Title MicMa_083
Sample type RNA
 
Source name Fresh frozen tumor biopsies from early breast cancer cases (Oslo I study, subtype: Normal-like)
Organism Homo sapiens
Characteristics diagnosis: early breast cancer
subtype: Normal-like
sample: MicMa_083
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Cy3
Label protocol 1µg RNA were analyzed on nONCOchip 1.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protocol) with the adaptation of using an N6 − T 7 primer instead of a polyT-T7 primer.
 
Hybridization protocol nONCOchip 1.0 arrays were proceed using the Agilent Hybridization Kit, Agilent Hybrization-Chambers and an commercial Hyb-Oven according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling Kit).
Scan protocol Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 2.32-2.43, PMT: 400, resolution: 5µm, Focus: 1µm, Lines to Average: 2, Wavelength: 532nm, Filter: Standard Green.
Description Expression analysis of 5 Normal-like breast cancer patient samples. 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.). 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 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.
Data processing The data were analyzed with R (version 2.14.2) and BioConductor. Expression levels were quantile normalized and a linear model was fitted using the R package limma in order to identify differentially expressed probes. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.
 
Submission date Aug 29, 2013
Last update date Jan 23, 2015
Contact name Kristin Reiche
E-mail(s) kristin.reiche@izi.fraunhofer.de
Organization name Fraunhofer Institute for Cell Therapy and Immunology
Department Diagnostics
Street address Perlickstr. 1
City Leipzig
ZIP/Postal code 04103
Country Germany
 
Platform ID GPL13648
Series (1)
GSE50428 Expression and differential expression analysis of breast cancer patient samples and normal samples

Data table header descriptions
ID_REF
VALUE quantile normalized values

Data table
ID_REF VALUE
243504 15.9999779860527
242592 15.9999779860527
241680 6.80839710516477
240768 6.80839710516477
239856 6.7982082333363
238944 8.28739384740923
238032 6.50082465448928
237120 6.54463535623544
236208 7.77798718596357
235296 7.94589721635841
234384 6.54463535623544
233472 7.37040708733257
232560 7.95078091266197
231648 6.358757883457
230736 7.41781659026651
229824 6.71069219821989
228912 6.38574814442408
228000 7.52400702024753
227088 9.00195878505122
226176 7.58519729446894

Total number of rows: 243504

Table truncated, full table size 5572 Kbytes.




Supplementary file Size Download File type/resource
GSM1219109_MicMa-083.gpr.gz 14.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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