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Sample GSM2773206 Query DataSets for GSM2773206
Status Public on Nov 15, 2018
Title small intestine_KO-2
Sample type RNA
 
Source name small intestine from Cyp3a-cluster knockout (Cyp3a-/-) mouse, KO, replicate 2
Organism Mus musculus
Characteristics tissue: small intestine
genotype: Cyp3a-/-
Extracted molecule total RNA
Extraction protocol Total RNA from small intestine of wild type or Cyp3a-/- mice was prepared using ISOGEN (Nippon Gene, Tokyo, Japan) and treated with RNase-free DNase I (Wako Pure Chemicals, Osaka, Japan), and were then purified using RNeasy columns (Qiagen, Hilden, Germany), in accordance with the manufacturer’s instructions.The concentration of the obtained total RNA was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). RNA quality was determined using the RNA ScreenTape and Reagent Kit (Agilent Technologies, Palo Alto, CA, USA) and an Agilent 2200 TapeStation (Agilent Technologies), and RNA was stored in RNase-free water at -80ºC.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 μg total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA, USA). Dye incorporation and cRNA yield were checked with the Nanodrop spectrophotometer.
 
Hybridization protocol Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containig 10×Blocking Agent, Nuclease-free water, and 25×Fragmentation Buffer following the manufature's instructions. On completion of the fragmentation reaction, 55 μl of 2×GE Hybridization Buffer (HI-RPM) was added to the fragmentation mixture and hybridized to 44K Agilent Whole Human Genome Oligo Microarays (G4846A) containing 44,397 features representing 39,429 biological probes for 17 hours at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minutes at room temparature with GE Wash Buffer 1 and 1 minute with 37°C GE Wash Buffer 2 (Agilent Technologies).
Scan protocol After washing microarrays according to manufacture's instructions, microarray slides were scanned immediately on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 4×44K array slides (Scan Area 61×21.6 mm, Scan resolution 5 μm, Dye channel is set to green, and 20 bit scan mode (no XDR scan mode)).
Data processing The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 026655_D_F_20140728). The data from all microarrays were analyzed using GeneSpringGX 14.5 (Agilent Technologies). After data transformation (to convert any negative value to 0.01), Intensity value of green Processedsignal from the Feature Extraction was normalized per chip to the 75th percentile.
 
Submission date Sep 06, 2017
Last update date Nov 15, 2018
Contact name Rumiko SAITO
E-mail(s) rumiko-s@med.tohoku.ac.jp
Organization name Tohoku University Graduate School of Medicine
Department Department of Dermatology
Street address 1-1 Seiryo-machi, Aoba-ku
City Sendai
ZIP/Postal code 980-8574
Country Japan
 
Platform ID GPL11202
Series (2)
GSE103534 Effect of Cyp3a-cluster knockout on small intestine
GSE103696 Endogenous gene expression profiling of Cyp3a-cluster knockout mice

Data table header descriptions
ID_REF
VALUE Normalized value was shown by the log2.

Data table
ID_REF VALUE
A_55_P1989846 0.337
A_55_P1991598 0.560
A_55_P2022211 0.372
A_55_P1980764 -1.289
A_55_P1964375 -0.023
A_51_P128876 0.222
A_55_P2121042 0.091
A_52_P219230 0.537
A_51_P207591 2.107
A_55_P2131920 -1.332
A_55_P2404223 -0.539
A_55_P2101944 0.471
A_52_P358860 -0.187
A_51_P119031 -0.058
A_51_P309854 0.523
A_51_P343900 0.175
A_51_P234359 -0.356
A_51_P487813 -0.014
A_52_P613977 0.100
A_55_P1957209 0.522

Total number of rows: 39408

Table truncated, full table size 768 Kbytes.




Supplementary file Size Download File type/resource
GSM2773206_small_intestine_KO-2.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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