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Sample GSM1885782 Query DataSets for GSM1885782
Status Public on Aug 10, 2016
Title Sample_486 UC_NA_Cecum
Sample type RNA
 
Source name Cecum
Organism Homo sapiens
Characteristics patient id: 262214
disease: UC
inflamed (0=no, 1=yes): NA
nanostring codeset: IBD3
Treatment protocol At the time of endoscopy, mucosal biopsies were collected in RNA-later (Qiagen) and stored at -80°C ahead of downstream processing. If samples were collected at the time of surgery, mucosal tissue sample obtained from bowel resection specimens with colonoscopic biopsy forceps were processed immediately or stored at 4°C for processing within 12 hours. Intestinal source location and inflammation status was indicated as “uninflamed” or “inflamed” based on the endoscopic or gross appearance of the tissue by the endoscopist or investigator at time of surgical specimen collection.
Extracted molecule polyA RNA
Extraction protocol Using a combined Trizol (Life Technologies)-chloroform extraction and the RNeasy Midi Kit (Qiagen) for RNA extraction, total RNA was extracted by manufacturer’s protocol and RNA purity and quantity was measured by NanoDrop spectrophotometer (Promega).
Label N/A
Label protocol Extracted RNA (100ng) was used as input for expression profiling on the NanoString platform according to manufacturer's specifications.
 
Hybridization protocol according to the manufacturer’s protocol
Scan protocol according to the manufacturer’s protocol
Description UC_NA_Cecum
Data processing Data from each version of probeset (lot) was first independently normalized and samples were analyzed for quality controls using following steps.
Background noise was estimated using mean expression levels of spiked-in negative controls
Estimated noise value was subtracted from raw counts data for each sample. Negative count values were reset to 1
Count values of spike-in positive controls were summed per sample and the average value was used to estimate a scaling factor for each sample. Expression value of each sample was adjusted using the sample specific normalization factor
Samples with higher than acceptable background noise and positive control based scaling factor <0.3 or >3.0 were identified as outliers and removed from analysis
Next, geometric mean of housekeeping genes was computed for each sample and the average value was used to compute the normalization factor. Data was adjusted in a similar fashion as was done previously with spiked-in positive controls
Finally, samples with housekeeping-genes based normalization factor <0.2 or >5.0 were removed as outliers.
Data Lots 2 & 3 were independently calibrated to Lot 1 using following steps.
The average of medians of calibration samples, for a given pair of lots, was computed and used to estimate normalization factor for each sample.
Each lot was scaled with the normalization factor computed in the previous step.
Geometric means of counts per gene between repeated samples was computed within a lot and a calibration factor was estimated per gene.
Calibration per gene was applied for the non-reference lot. All computations were performed in MATLAB. Nine hundred and eighty-nine samples passed data normalization and quality control.
 
Submission date Sep 16, 2015
Last update date Aug 11, 2016
Contact name Ramnik J Xavier
E-mail(s) xavier@molbio.mgh.harvard.edu
Organization name Massachusetts General Hospital
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL20926
Series (1)
GSE73094 Genes in Inflammatory Bowel Disease-Associated Risk Loci Demonstrate Genotype-, Tissue-, and Inflammation-Specific Patterns of Expression in Terminal Ileum and Colon Mucosal Tissue

Data table header descriptions
ID_REF
VALUE Normalized expression data (Log2 scale)

Data table
ID_REF VALUE
A3GALT2 3.3375
AAMP 9.3278
ABCB5 4.8231
ACCN5 1.5232
ACSL6 5.1176
ADA 5.3034
ADAD1 2.975
ADAM30 -1.7743
ADCY3 6.5802
ADCY7 8.0286
ADO 8.0483
AFF3 6.2662
AGAP2 1.4161
AHRR 7.1014
AHSA2 8.9524
AIF1 7.1323
AIRE_v1 3.1303
AIRE_v2 1.35
AKAP11 9.0733
AMIGO3 1.7361

Total number of rows: 712

Table truncated, full table size 9 Kbytes.




Supplementary file Size Download File type/resource
GSM1885782_Sample_486.txt.gz 4.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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