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Sample GSM1034122 Query DataSets for GSM1034122
Status Public on Nov 21, 2012
Title gmcsf ko dss 6 days 80_4
Sample type RNA
 
Source name colon crypts from 1.5%DSS treated gmcsf ko mice for 6 days
Organism Mus musculus
Characteristics genotype: GMCSF KO
treatment: DSS
gender: male
tissue: colon crypts
strain: C57BL/6
age: 8 weeks
Treatment protocol Colitis was induced by allowing mice to drink 1.5% (w/v) Dextran sodium sulfate (DSS) (m. w. 36-50 kDa, MP Biomedicals) dissolved in the drinking water ad libitum for 6 days. Untreated mice were administered water only.
Extracted molecule total RNA
Extraction protocol Total RNA (isolated by RNeasy kit; Qiagen following the manufacturer's intructions) was prepared from isolated crypts of WT and GM-CSF-/- mice colons before or after 1.5% DSS treatment for 6 days. .
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Quick Amplification Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1650ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray Kit, 4x44K (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B). 5 µm scanning in green at 10% and 100% PMT
Data processing Slide design ID was 26655 and the protocol used for extraction was GE1_107_Sep09. Version 10.7.3.1. of feature extraction. The data were normalized using the multi-loess method described in this paper: Microarray truths and consequences, R. Sasik, C. H. Woelk and J. Corbeil, J. Mol. Endocrinology, 33, 1 (2004)
 
Submission date Nov 08, 2012
Last update date Nov 21, 2012
Contact name Laia Egea
E-mail(s) legeapujol@ucsd.edu
Organization name UCSD
Department Medicine
Lab Laboratory of Mucosal Immunology
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093-0623
Country USA
 
Platform ID GPL10333
Series (1)
GSE42173 Expression profile of colon crypts from WT and GMCSF-/- mice with or without DSS treatment

Data table header descriptions
ID_REF
VALUE Agilent Feature Extraction default normalized signal intensity

Data table
ID_REF VALUE
1 1.35E+04
2 3.80E+00
3 3.80E+00
4 3.80E+00
5 3.80E+00
6 3.80E+00
7 3.80E+00
8 3.81E+00
9 3.81E+00
10 3.81E+00
11 3.82E+00
12 5.59E+00
13 3.82E+00
14 8.25E+00
15 2.25E+01
16 2.80E+03
17 1.53E+03
18 9.61E+03
19 3.87E+00
20 1.65E+04

Total number of rows: 44397

Table truncated, full table size 639 Kbytes.




Supplementary file Size Download File type/resource
GSM1034122_US22502657_252665512580_S01_GE1_107_Sep09_1_4.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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