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Sample GSM1180582 Query DataSets for GSM1180582
Status Public on Apr 17, 2014
Title WT, biological rep2
Sample type RNA
 
Source name DSS-treated colons derived from WT mice
Organism Mus musculus
Characteristics strain/background: C57BL/6J
genotype/variation: wild type
age: fourteen weeks
tissue: colon
treatment: DSS
Treatment protocol Wild type (WT) and STAP-2-/- mice were administered 1.75% DSS for 3 days and sacrificed to isolate mRNA from colon tissue.
Extracted molecule total RNA
Extraction protocol Total RNA of the entire colon tissues, which was immediately stored in RNAlater solution at -80 °C (Life Technologies, Carlsbad, CA), was purified using TissueLyser at 20 Hz and RNeasy kit (QIAGEN, Venlo, Netherlands) according to the manufacturer's instructions.
Label Cy3
Label protocol One hundred nanogram of total RNA with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent Technologies) was reverse transcribed into double strand cDNAs by AffinityScript multiple temperature reverse transcriptase and amplified for 2 h at 40°C. Resulting cDNAs were subsequently used for in vitro transcription by T7-polymerase and labeled with cyanine-3-labeled cytosine triphosphate (Perkin Elmer) for 2 h at 40°C using a Low Input Quick-Amp Labeling Kit ver. 6.5 (Agilent Technologies) according to the manufacturer's protocol.
 
Hybridization protocol After labeling, rates of dye incorporation and quantification were measured with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and were then fragmented for 30 min at 60°C in the dark. The labeled 1,650 ng of each cRNA sample was then hybridized on Agilent 4 × 44K whole mouse genome arrays (Agilent Design #026655) at 65°C for 17 h with rotation in the dark. Hybridization was performed using a Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturer's instructions.
Scan protocol After washing in GE washing buffer, slides were scanned with an Agilent Microarray Scanner G2505C.
Description WT2
Acute colitis model was induced to WT mice by addition of 1.75% DSS in drinking water for 7 days.
Pool from 3 mice.
Data processing Feature Extraction software (Version 10.7.1.1) employing defaults for all parameters was used to convert images into gene expression data. Raw data were imported into GeneSpring GX 12.0 (Agilent Technologies) for database management and quality control. For normalization in GeneSpring, the threshold raw signal was set to 1.0 and the global normalization algorithm (percentile shift) was used with a percentile target of 75. This normalized data was used for identifying differentially expressed genes, in which KO group were compared to WT group as control.
 
Submission date Jul 03, 2013
Last update date Apr 17, 2014
Contact name Daisuke Okuzaki
E-mail(s) dokuzaki@biken.osaka-u.ac.jp
Phone +81-6-6879-4935
Organization name Osaka univ.
Department Immunology Frontier Research Center
Lab Human Immunology (Single Cell Genomics)
Street address Yamadaoka 3-1
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
 
Platform ID GPL11202
Series (1)
GSE48543 Microarray analysis of colon tissue of DSS colitis STAP-2 KO mice

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
(-)3xSLv1 0.003
(+)E1A_r60_1 229.792
(+)E1A_r60_3 0.003
(+)E1A_r60_a104 0.003
(+)E1A_r60_a107 0.038
(+)E1A_r60_a135 0.258
(+)E1A_r60_a20 0.617
(+)E1A_r60_a22 1.741
(+)E1A_r60_a97 8.820
(+)E1A_r60_n11 36.076
(+)E1A_r60_n9 68.742
A_51_P100034 4.097
A_51_P100174 0.175
A_51_P100208 0.005
A_51_P100289 2.073
A_51_P100298 0.321
A_51_P100309 0.002
A_51_P100327 0.142
A_51_P100347 0.008
A_51_P100519 0.002

Total number of rows: 39485

Table truncated, full table size 758 Kbytes.




Supplementary file Size Download File type/resource
GSM1180582_WT_2_normalized_.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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