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Sample GSM1017659 Query DataSets for GSM1017659
Status Public on Aug 09, 2013
Title MEF_Wapl(+/F)_4
Sample type RNA
 
Channel 1
Source name G0 phase synchronized MEFs
Organism Mus musculus
Characteristics strain: mixed C57BL/6 and 129
cell type: G0 phase synchronized MEFs
age: 13.5 dpc
sample group: B4
genotype: Wapl (+/F) ERCre/+
treatment: starvation
hybridisation chip: 58MM
Treatment protocol 4-OHT was added to the starvation medium to a final concentration of 500 nM
Growth protocol MEFs were starved in OptMEM containing 2% serum for seven days before RNA extraction
Extracted molecule total RNA
Extraction protocol Total RNA extracted using RNeasy Mini Kit (QIAGEN) following manufacturer's instructions
Label Cy3
Label protocol Labeling with a Reactive Fluorescent Dye/ Molecular probes (Alexa 555, 647) Thoroughly dissolve the amine-modified 4µg DNA in 5µl nuclease free H2O (warming to 42°C for 5 min if necessary) Add 3µl Labeling buffer (Just before use dissolve one vial of reactive dye in 10-20µl DMSO or use aliquots from –80°C) Add 2µl reactive dye to the samples, vortex briefly to mix (do not spin) Incubate for 1 hour in the dark at room temperature
 
Channel 2
Source name pool
Organism Mus musculus
Characteristics reference: pool
Treatment protocol 4-OHT was added to the starvation medium to a final concentration of 500 nM
Growth protocol MEFs were starved in OptMEM containing 2% serum for seven days before RNA extraction
Extracted molecule total RNA
Extraction protocol Total RNA extracted using RNeasy Mini Kit (QIAGEN) following manufacturer's instructions
Label Cy5
Label protocol Labeling with a Reactive Fluorescent Dye/ Molecular probes (Alexa 555, 647) Thoroughly dissolve the amine-modified 4µg DNA in 5µl nuclease free H2O (warming to 42°C for 5 min if necessary) Add 3µl Labeling buffer (Just before use dissolve one vial of reactive dye in 10-20µl DMSO or use aliquots from –80°C) Add 2µl reactive dye to the samples, vortex briefly to mix (do not spin) Incubate for 1 hour in the dark at room temperature
 
 
Hybridization protocol Probe- Prehybridisation (TECAN HS4800) Protocol for 40 domain chips: Combine: 50µl Labeled DNA 29µl 20x SSPE 4µl 50x Denhardts solution 50µl Form amid 1.5µl mouse block 3.5µl 20% SDS (last component to be added) Incubate at 94°C for 2 min Prehybridise probe for at least 1 hour at 50°C • start prehybridization of the slides • After prehyb of the samples and the slides pipette 135 µl onto each slide If you have duplicates then pool and use 135µl per slide • split and pipette 140 µl onto each slide • Continue with hybridization on TECAN HS4800 for 12hours 45°C
Scan protocol Scanner: GenePix 4000B
Description Wapl (+/F)
Data processing Image Analysis: GenPix Pro 6.0. Data analysis: The statistical computing software R version 2.11.0 http://www.R-project.org and the limma package [Smyth 2004] was used for data normalization and calculation of fold changes and differential expression. In brief, we first removed all clones with missing signal intensities. Micro Array expression intensities were then background corrected using RMA and normalized within arrays with default settings. Only clones with reasonable (>250) expression values in at least 25% of the samples were analyzed further. Differentially expressed genes were obtained by applying limma's linear model fit and subsequent Benjamini Hochberg p-value adjustment. Genes with adjusted p-value smaller than 0.01 were called significant.
 
Submission date Oct 10, 2012
Last update date Aug 09, 2013
Contact name Roman R Stocsits
E-mail(s) roman.stocsits@imp.ac.at
Organization name IMP - Research Institute of Molecular Pathology
Lab Jan-Michael Peters' Lab
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL16159
Series (2)
GSE41460 Wapl controls higher-order chromatin structure in interphase chromosomes (gene expression)
GSE41603 Wapl controls higher-order chromatin structure in interphase chromosomes

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

Data table
ID_REF VALUE
1
2 -0.730377514
3
4
5
6
7
8 -0.280928857
9
10 -0.769018181
11 -0.431903472
12 -0.208790122
13 0.108050822
14 -2.058821469
15 -0.329751691
16
17 -0.616113449
18 0.083984705
19
20 0.05660255

Total number of rows: 23695

Table truncated, full table size 409 Kbytes.




Supplementary file Size Download File type/resource
GSM1017659_58MM371793.gpr.gz 2.0 Mb (ftp)(http) GPR
Processed data included within Sample table

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