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Sample GSM377741 Query DataSets for GSM377741
Status Public on Mar 05, 2009
Title Butyrate_rep3_Cy5
Sample type RNA
Source name R1 mESC
Organism Mus musculus
Characteristics cell type: mouse embryo stem cells
cell line: R1
Treatment protocol Independent quadruplicate: groupA in LIF (Chemicon) without feeders, groupB in 0.2mM sodium butyrate (without LIF) for 15 passages
Growth protocol mESC in DMEM, 15% serum replacer, glutamax, pen/strep, NEAA, pyruvate (Invitrogen) and mercaptoethanol (Sigma), grown on gelatin (Sigma) at 37C in 5% CO2
Extracted molecule total RNA
Extraction protocol RNA extraction utilized the Rneasy Minikit (Qiagen) following manufacturer's protocol. The RNA was treated with Dnase and given to the Center for Array Technologies for quantitation and purity analysis.
Label Cy5
Label protocol Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the Low RNA Input Linear Amplification PLUS 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 825ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) and 825ng of Cy5-labelled cRNA (specific activity >10.0 pmol Cy5/ug cRNA) were combined and fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) and Agilent Whole Genome Mouse Microarrays (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 compressed nitrogen (N2) gun.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Red and both Green PMT and Red PMT arer set to 100%).
Description Gene Expression after exposure to Butyrate
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Mar 04, 2009
Last update date Mar 04, 2009
Contact name Brig Mecham
Organization name University of Washington
Street address 1100 Fairview Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
Platform ID GPL4134
Series (2)
GSE15107 R1 mESC Exposed to Butyrate
GSE15112 ESC Exposed to Butyrate

Data table header descriptions
VALUE Normalized signal intensity

Data table
12 2.718
13 6.128
14 3.006
15 2.888
16 10.749
18 2.782
19 2.791
20 2.8
21 2.807
22 11.12
23 2.819
24 8.499
25 5.215
26 9.116
27 8.803
28 4.705
29 9.051
30 2.852
31 2.855
32 2.86

Total number of rows: 43379

Table truncated, full table size 504 Kbytes.

Supplementary file Size Download File type/resource
GSM377741_US23502338_251486811295_S01_H_GE2-v5_95_Feb07_1_3_Cy5.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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