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Sample GSM1081865 Query DataSets for GSM1081865
Status Public on May 08, 2013
Title 11-1667_(miRNA-2_0)
Sample type RNA
 
Source name Serum
Organism Homo sapiens
Characteristics batch: 15
chip_lot_ab: A
pair_index: 75
status: case
age: 47
race: 1) Non-Hispanic White
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was extracted in batches using the Total RNA purification kit. Each individual sample was split into two equal aliquots and then processed following the manufacture’s recommended protocol for total RNA purification from serum. An on-column DNase digestion was added before sample elution using the RNase-Free DNase I Kit, following the manufacturer’s instructions.
Label biotin
Label protocol 8µl of total RNA was directly labeled using The Flash Tag Biotin HSR Labeling kits following the manufacturer’s instructions. RNA was heated at 80° C for 10 min before labeling to inactivate any residual DNase activity.
 
Hybridization protocol RNA was hybridized for 42 hours to the GeneChip miRNA 2.0 array
Scan protocol The arrays were washed and stained using standard Affymetrix protocols and scanned using the Affymetrix GCS 3000 7G Scanner. Feature intensities were extracted using the miRNA 2.0 array library files.
Description microRNA expression analyzed from total RNA extracted from serum
Data processing MiRNA expression intensity values were background corrected and normalized across arrays using the Robust Multichip Average (RMA) method. The intensity data used in all analysis were log (2) transformed. For each array the miRNA probe set signals were compared to the distribution of signals for anti-genomic probes that had matching GC content (miRNA QC Tool, Version 1.0.33.0) and following the manufacture’s recommendation, Wilcoxon Rank-Sum test of p<0.06 was used to identify miRNAs above background. Subsequent analysis was restricted to 414 miRNAs that exceeded background levels in at least 50 women. Conditional logistic regression was used to identify differentially expressed miRNA probes between cases and controls for those 414 probes.
 
Submission date Feb 12, 2013
Last update date May 09, 2013
Contact name Zongli Xu
Organization name NIH/NIEHS
Street address 111 tw alexander Dr.
City Research Triangle Park
ZIP/Postal code 27709
Country USA
 
Platform ID GPL14613
Series (1)
GSE44281 Serum microRNA expression as an early marker for breast cancer risk in prospectively collected samples from the Sister Study cohort

Data table header descriptions
ID_REF
VALUE normalized signal
p-value (11-1667_(miRNA-2_0).CEL)
Detection (11-1667_(miRNA-2_0).CEL)

Data table
ID_REF VALUE p-value (11-1667_(miRNA-2_0).CEL) Detection (11-1667_(miRNA-2_0).CEL)
14q0_st 1.558801 0.3567411 FALSE
14qI-1_st 5.472186 1.16E-05 TRUE
14qI-1_x_st 4.788772 2.12E-05 TRUE
14qI-2_st 1.206234 0.6387997 FALSE
14qI-3_x_st 1.406533 0.8312938 FALSE
14qI-4_st 1.507758 0.2622386 FALSE
14qI-4_x_st 1.222108 0.9056885 FALSE
14qI-5_st 1.317126 0.5907483 FALSE
14qI-6_st 1.283465 0.9652793 FALSE
14qI-6_x_st 1.853022 0.4127623 FALSE
14qI-7_st 1.562768 0.5372623 FALSE
14qI-8_st 1.695092 0.4670099 FALSE
14qI-8_x_st 1.12518 0.8490758 FALSE
14qI-9_x_st 1.249404 0.8343638 FALSE
14qII-10_st 1.549239 0.1072965 FALSE
14qII-10_x_st 1.615902 0.3904327 FALSE
14qII-11_st 1.658545 0.7068077 FALSE
14qII-11_x_st 1.038278 0.6676756 FALSE
14qII-12_st 1.222493 0.8200666 FALSE
14qII-12_x_st 1.026643 0.8888701 FALSE

Total number of rows: 20180

Table truncated, full table size 819 Kbytes.




Supplementary file Size Download File type/resource
GSM1081865_11-1667_miRNA-2_0_.CEL.gz 607.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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