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Sample GSM736780 Query DataSets for GSM736780
Status Public on Aug 01, 2012
Title 16508-11F
Sample type RNA
 
Source name Colon Tissue from patient with Crohn's disease
Organism Homo sapiens
Characteristics disease: Chron's Disease
dategroup of array: A
cd68 expression: High
nos2 expression: High
Extracted molecule total RNA
Extraction protocol Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.
Label Biotin
Label protocol Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.
 
Hybridization protocol Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.
Scan protocol Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.
Description CD68 and NOS2 were measured by qRT-PCR and dichotomized as high/low based on median expression levels Crohn's disease and Ulcerative Colitis separately. Missing values were dropped from analysis.
Data processing The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 2.0). Intensities of each spot were the median intensities of foreground. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. Each microRNA oligo is represented by quadruplicate spots on these arrays as two distant pairs of two adjacent spots. If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package and all replicate spots were averaged. Batch effects caused by day to day variability was removed using Partek Genomics Suite.
 
Submission date Jun 02, 2011
Last update date Aug 01, 2012
Contact name Aaron Schetter
E-mail(s) schettera@mail.nih.gov
Organization name National Cancer Institute
Department Laboratory of Human Carcinogenesis
Street address 37 Convent Drive, Building 37, Room 3050
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL13681
Series (1)
GSE29703 Association of microRNAs with CD68 and NOS2 in IBD tissues.

Data table header descriptions
ID_REF
VALUE LOESS Normalized signal intensity with batch effect correction using Partek Genomics Suite

Data table
ID_REF VALUE
hsa-mir-033b-prec 9.76043
hsa-mir-034precNo1 8.77181
hsa-mir-092-prec-13=092-1No1 8.70958
hsa-mir-092-prec-x=092-2 10.8139
hsa-mir-095-prec-4 8.75924
hsa-mir-096-prec-7No2 10.7901
hsa-mir-107-prec-10 9.67545
hsa-mir-123-precNo1 8.5481
hsa-mir-124a-1-prec1
hsa-mir-124a-3-prec
hsa-mir-125a-precNo2
hsa-mir-125b-2-precNo1 8.22577
hsa-mir-133a-2 8.5294
hsa-mir-134-precNo2
hsa-mir-135-2-prec
hsa-mir-136-precNo2 9.59213
hsa-mir-138-1-prec
hsa-mir-139-prec
hsa-mir-150-prec 9.61655
hsa-mir-152-precNo1

Total number of rows: 1780

Table truncated, full table size 29 Kbytes.




Supplementary file Size Download File type/resource
GSM736780.gpr.gz 432.4 Kb (ftp)(http) GPR
Processed data included within Sample table

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