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Sample GSM358738 Query DataSets for GSM358738
Status Public on Jun 15, 2009
Title CHIPnull_240m_Heatshock_rep2
Sample type RNA
 
Channel 1
Source name CHIP(-/-) MEF, heat shock, 240 min
Organism Mus musculus
Characteristics embryonic fibroblast
Treatment protocol MEF cultures were either maintained at 37° C or heat shocked at 43° C for the indicated time points prior to RNA harvesting.
Growth protocol MEFs (mouse embryonic fibroblasts) isolated from day 13.5 embryos of C57BL6 CHIP (+/-) crosses were grown under similar conditions with the addition of β-mercaptoethanol at 37° C, 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was purified using the RNeasy microkit (Qiagen) in accordance with the manufacturer’s instructions which included DNase treatment to eliminate genomic contamination. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer.
Label Cy5
Label protocol 500 ng of total RNA from three biological replicates from each condition were used for amplification and labeled with Cy5 using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.
 
Channel 2
Source name Stratagene UMRR
Organism Mus musculus
Characteristics pool of mouse reference RNA
Treatment protocol MEF cultures were either maintained at 37° C or heat shocked at 43° C for the indicated time points prior to RNA harvesting.
Growth protocol MEFs (mouse embryonic fibroblasts) isolated from day 13.5 embryos of C57BL6 CHIP (+/-) crosses were grown under similar conditions with the addition of β-mercaptoethanol at 37° C, 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was purified using the RNeasy microkit (Qiagen) in accordance with the manufacturer’s instructions which included DNase treatment to eliminate genomic contamination. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer.
Label Cy3
Label protocol 500 ng of total RNA from three biological replicates from each condition were used for amplification and labeled with Cy5 using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.
 
 
Hybridization protocol Labeled cRNA was co-hybridized to Agilent G4122F Whole Mouse Genome 44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UMRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.
Scan protocol Scanned on an Axon Instruments GenePix 4000b scanner.
Description none
Data processing The data were processed using Feature Extraction software and normalized using per-chip and per-spot intensity-dependent LOWESS normalization with a threshold of 0.01. The data at the two heat shock time-points, 30 and 240 minutes, were normalized by their respective un-shocked controls.
 
Submission date Jan 08, 2009
Last update date Jun 15, 2009
Contact name Jonathan C Schisler
E-mail(s) schisler@unc.edu
Phone 919-843-8708
Organization name The University of North Carolina at Chapel Hill
Department McAllister Heart Institute
Lab Schisler Lab
Street address MBRB, Rm 2340C
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7126
Country USA
 
Platform ID GPL7202
Series (1)
GSE14339 Stress-dependent CHIP/Daxx interaction suppresses the p53 apoptotic program

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing sample/reference

Data table
ID_REF VALUE
A_52_P467389 0.170998676
A_52_P214034 0.407309272
A_51_P340174 0.411195137
A_51_P113475 0.299769539
A_52_P622850 0.155028327
A_52_P199614 0.331392915
A_52_P172014 0.216760972
A_51_P371750 -0.057024208
A_51_P319917 -0.137534342
A_51_P298266 0.193921761
A_51_P176154 0.150570737
A_51_P174996 0.418578705
A_51_P149714 0.103103513
A_51_P147274 0.179159946
A_51_P131358 0.39666882
A_52_P980644 0.343043791
A_52_P900402 0.548810418
A_52_P625640 0.736225696
A_52_P408518 0.272746009
A_51_P323812 0.123893975

Total number of rows: 28139

Table truncated, full table size 694 Kbytes.




Supplementary file Size Download File type/resource
GSM358738.txt.gz 12.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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