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Sample GSM1363326 Query DataSets for GSM1363326
Status Public on Jan 15, 2015
Title SI50
Sample type RNA
Source name Epithelial tissue, small intestine
Organism Homo sapiens
Characteristics tissue: Small Intestine
Treatment protocol Not applicable
Growth protocol Not applicable
Extracted molecule total RNA
Extraction protocol Total RNA containing both miRNA and mRNA was extracted using the Qiagen miRNeasy kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s protocol. Only total RNA of highest quality and integrity was subjected to further processing after purification as defined by an absorption ratio 260/280>1.8 by spectrophotometry on the NanoDrop 1000 (NanoDrop, Wilmington, DE) and a RIN value >8.0 via electrophoretic analysis on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).
Label biotin
Label protocol RNA was quantified with the Nanodrop (Thermo Scientific, IL). Reverse transcription was performed using iScript RT Supermix followed by PCR with SsoADV SYBR Green (Bio-Rad, CA) on an ABI StepOne Plus Real-Time PCR machine (Applied Biosystems, CA). Primers were designed using Primer Express software (Applied Biosystems, CA) and purchased from Life Technologies (NY) (Table 3).
Hybridization protocol Fifteen micrograms of purified, amplified, biotin labeled cRNA was fragmented and hybridized on to Affymetrix Human Genome HGU133A 2.0 arrays (Affymetrix Corp. Santa Clara, CA) for 18 hours.
Scan protocol Washing, staining and scanning of arrays was performed on the Affymetrix Fluidics Station 450 and Scanner 3000 immediately after completion of hybridization.
Data processing Microarray data was processed using the Robust Multi-array Average by importing raw CEL files into Partek software (Partek Genomics Suite, St. Louis, MO) resulting in RMA background correction, log 2 transformation, quantile normalization, and median polish probeset summarization.
Submission date Apr 04, 2014
Last update date Jan 15, 2015
Contact name William Armand LaFramboise
Phone 412-623-6160
Organization name University of Pittsburgh
Department Pathology
Street address 5230 Centre Avenue
City Pittsburgh
State/province PA
ZIP/Postal code 15232
Country USA
Platform ID GPL571
Series (1)
GSE56525 Distinct human stem cell populations in small and large intestine

Data table header descriptions
VALUE RMA normalized expression data

Data table
1007_s_at 14.3937
1053_at 9.2353
117_at 8.80557
121_at 11.3961
1255_g_at 8.64303
1294_at 8.7619
1316_at 10.9425
1320_at 9.01758
1405_i_at 9.0224
1431_at 8.97683
1438_at 8.18907
1487_at 12.2337
1494_f_at 8.5404
1598_g_at 9.80441
160020_at 9.66216
1729_at 8.50997
1773_at 8.36741
177_at 10.2784
179_at 8.9414
1861_at 8.07799

Total number of rows: 22277

Table truncated, full table size 409 Kbytes.

Supplementary file Size Download File type/resource
GSM1363326_12_0265_HG-U133A_2_.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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