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Sample GSM1441440 Query DataSets for GSM1441440
Status Public on Jul 23, 2014
Title colon_DSS_day1_rep1
Sample type RNA
 
Channel 1
Source name colon_DSS_day1_rep1
Organism Mus musculus
Characteristics strain: c57BL/6
tissue: colon
genotype: wild type
group: DSS-d1
Treatment protocol Wild type c57BL/6 mice were fed ad libitum with 2.5% (wt/vol) dextran sodium sulfate (DSS, 40KDa, ICN Biochemicals, Aurora, OH) in drinking water for 1, 3 or 5 days to induce acute phase colitis. To induce chronic colitis, C57BL/6 mice were supplied with 2.5% DSS in drinking water for 5 days and switched back to normal drinking water for 9 days before the next cycles. Four cycles of the DSS treatment were used in the study.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Hy3
Label protocol not provided
 
Channel 2
Source name Total RNA from pooled from individual samples
Organism Mus musculus
Characteristics group: reference
Treatment protocol Wild type c57BL/6 mice were fed ad libitum with 2.5% (wt/vol) dextran sodium sulfate (DSS, 40KDa, ICN Biochemicals, Aurora, OH) in drinking water for 1, 3 or 5 days to induce acute phase colitis. To induce chronic colitis, C57BL/6 mice were supplied with 2.5% DSS in drinking water for 5 days and switched back to normal drinking water for 9 days before the next cycles. Four cycles of the DSS treatment were used in the study.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Hy5
Label protocol not provided
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
Scan protocol After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)
Description Hy3: Mice were sacrificed 1 day post DSS in drinking H2O.
DSS-d1_1
Data processing image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Annotation is based on miRBASE version 14.0
 
Submission date Jul 22, 2014
Last update date Jul 23, 2014
Contact name Yong Huang
E-mail(s) yh9fj@virginia.edu
Phone (434) 243-0842
Organization name University of Viginia
Department Medicine
Street address 1340 Jefferson Park Ave
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
 
Platform ID GPL7723
Series (2)
GSE59649 Divergent influence of microRNA-21 deletion on murine colitis phenotypes [DSS]
GSE59651 Divergent influence of microRNA-21 deletion on murine colitis phenotypes

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

Data table
ID_REF VALUE
27263 0.177772154
17888 0.109104258
17749 0.116617602
42769 0.050409838
19004 0.1643692
42668 -0.259338666
46437 0.074107333
42505 0.078563552
46436 0.044191801
46435 0.152659719
42768 null
46438 0.067654843
42778 null
9938 0.011265021
42534 null
10916 0.04757695
19581 -0.03515652
31026 -0.263806153
17935 null
42953 -0.217158327

Total number of rows: 665

Table truncated, full table size 9 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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