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Sample GSM1093538 Query DataSets for GSM1093538
Status Public on Jun 21, 2014
Title BRCAX_04T355
Sample type RNA
 
Source name hereditary invasive breast cancer
Organism Homo sapiens
Characteristics storage: formalin-fixed parafin-embeded tissue
tumor type: BRCAX breast tumor
Extracted molecule total RNA
Extraction protocol For each sample tumoral area was marked by pathologist, FFPE blocks were cut in 5x 30µm sections and tumor tissue was isolated by needle macrodissection for subsequent RNA extraction. Total RNA was extracted using miRNeasy FFPE kit (QIAGEN) according to manufacturer’s instructions, while tissue digestion step was performed using 20 mg/ul Proteinase K (Roche, Basel, Switzerland) for over-night incubation step at 55ºC. RNA quantity was assessed by NanoDrop Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
Label Hy3
Label protocol 300ng of total RNA were treated for with Calf Intestine Phosphatase and than labeled with Hy3 fluorescent dye according to manufacturers instructions.
 
Hybridization protocol Denaturated Hy3 labeled RNA samples in 1x hybridization buffer were hybridized at 56ºC for 16h onto Exiqon miRNA microarray slides (v.11.0 – hsa, mmu & rno) containing 1940 capture probes in 4 replicates, including 830 human miRNAs annotated in miRBasev.11 database and 434 hsa- miRPlus probes. A set of 10 synthetic spike-in RNAs was added to total RNA sample prior to labeling and later used for quality control.
Scan protocol Processed slides were scanned with Agilent Array scanner (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635nm, at Power 80 and PMT 70 setting, and a scan resolution of 10μm.
Data processing Fluorescence intensities on scanned images were quantified using Feature Extraction software (Agilent Technologies, Santa Clara, CA, USA) using the modified Exiqon protocol. Average processed intensity values of the replicate spots were background subtracted using Normexp, and log2 transformed. Raw data were quantile normalized for inter-array variability using R/Bioconductor. Data was further processed to eliminate miRNAs with uniformly low expression (<6.5) or with low expression variation (VAR<0.1) across the experiments, retaining 444 miRNA genes (276 hsa-miR + 168 hsa-miRPlus).
 
Submission date Mar 05, 2013
Last update date Jun 21, 2014
Contact name Miljana Tanic
E-mail(s) tanic.miljana@gmail.com
Organization name Institute for Oncology and Radiology of Serbia (IORS)
Department Experimental Oncology
Lab Laboratory of Molecular Genetics
Street address Pasterova 14
City Belgrade
ZIP/Postal code 11000
Country Serbia
 
Platform ID GPL7723
Series (1)
GSE44899 miRNA expression profiling in hereditary breast tumors

Data table header descriptions
ID_REF
VALUE Quantile-normalized log2 transformed signal intensity

Data table
ID_REF VALUE
17748 8.515705185
17888 7.497842596
42769 8.092274684
17749 9.014593033
19004 9.424221307
46437 7.211108494
46436 9.402248359
46435 9.685716296
46438 7.523423629
9938 7.803783778
19581 6.0941146
31026 6.180097068
10919 6.444639386
42648 6.391156188
19582 6.373786822
10923 6.63563349
13485 6.524504427
46258 6.854976049
46345 8.260413424
19583 9.354588186

Total number of rows: 444

Table truncated, full table size 7 Kbytes.




Supplementary file Size Download File type/resource
GSM1093538_US22502553_14125129_S01_fliped_Exiqon_SingleColor.txt.gz 780.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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