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Sample GSM1302311 Query DataSets for GSM1302311
Status Public on Dec 31, 2014
Title Non-IBD_colonbiopsy_rep1
Sample type RNA
 
Channel 1
Source name Colon pinch biopsy
Organism Homo sapiens
Characteristics disease state: normal
tissue: Colon
Extracted molecule total RNA
Extraction protocol Total RNA extracted using miRNeasy kit following manufacturer's instructions
Label Hy3
Label protocol The samples were labeled using the miRCURY™ Hy3/Hy5 Power labeling kit. Individual samples were labeled with Hy3 (test) while the reference sample (containing equal amounts of RNA from all 5 samples) was labeled with Hy5.
 
Channel 2
Source name Total RNA from pooled colon biopsies.
Organism Homo sapiens
Characteristics sample type: Total RNA from pooled colon biopsies.
tissue: Colon
Extracted molecule total RNA
Extraction protocol Total RNA extracted using miRNeasy kit following manufacturer's instructions
Label Hy5
Label protocol The samples were labeled using the miRCURY™ Hy3/Hy5 Power labeling kit. Individual samples were labeled with Hy3 (test) while the reference sample (containing equal amounts of RNA from all 5 samples) was labeled with Hy5.
 
 
Hybridization protocol The samples were hybridized on the miRCURY™ LNA Array (version 5th Generation arrays, hsa, mmu and rno). Analysis of the scanned slides showed that the labeling was successful as all capture probes for the control spike-in oligo nucleotides produced signals in the expected range.
Scan protocol The quantified signals (background corrected) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm, which we have found produces the best within-slide normalization to minimize the intensity-dependent differences between the dyes. The positive effect of this normalization is illustrated in the MA-plots for each slide. An example is found in section 3 in this document (all MA plots are found in the folder named ‟Graphics‟).
Description Biological replicate 1 of 1. Control non-IBD colon biopsy.
Data processing The quantified signals (background corrected) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm, which we have found produces the best within-slide normalization to minimize the intensity-dependent differences between the dyes. The positive effect of this normalization is illustrated in the MA-plots for each slide. An example is found in section 3 in this document (all MA plots are found in the folder named ‟Graphics‟).
 
Submission date Jan 07, 2014
Last update date Dec 31, 2014
Contact name Jeremy S Schaefer
E-mail(s) Jeremy.Schaefer@uth.tmc.edu
Phone 713-486-4107
Organization name The University of Texas Health Science Center at Houston School of Dentistry
Department Diagnostic Sciences
Lab John Klein
Street address 1941 East Rd
City Houston
State/province TX
ZIP/Postal code 77054
Country USA
 
Platform ID GPL14149
Series (1)
GSE53867 MicroRNA expression in human colon: Crohn's disease versus ulcerative colitis

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Hy3/Hy5) representing test/reference

Data table
ID_REF VALUE
46715 -0.06
46523 0.41
42661 -0.26
46723 null
46642 -0.04
17653 null
42566 null
21526 0.63
146140 -0.20
42827 null
28889 null
145962 0.09
145755 null
42929 -0.25
46718 null
145724 null
46499 null
42743 null
145978 -0.44
13177 0.28

Total number of rows: 1409

Table truncated, full table size 15 Kbytes.




Supplementary file Size Download File type/resource
GSM1302311_0_Exiqon_14173049_S01.txt.gz 839.6 Kb (ftp)(http) TXT
GSM1302311_1_Exiqon_14173049_S01.txt.gz 903.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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