|
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 |
|