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Sample GSM1093557 Query DataSets for GSM1093557
Status Public on Jun 21, 2014
Title BRCAX_04T400
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 8.508760391
17888 6.829295612
42769 6.733807524
17749 8.19257503
19004 9.749433398
46437 7.764086828
46436 10.04956957
46435 9.541517036
46438 7.199413343
9938 7.382743701
19581 6.222792017
31026 6.270052437
10919 7.522463494
42648 6.650668257
19582 6.701067898
10923 7.020777177
13485 6.543769365
46258 7.304396471
46345 6.864273325
19583 7.738773267

Total number of rows: 444

Table truncated, full table size 7 Kbytes.




Supplementary file Size Download File type/resource
GSM1093557_US22502553_14125149_S01_fliped_Exiqon_SingleColor.txt.gz 803.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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