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Sample GSM3188631 Query DataSets for GSM3188631
Status Public on Jun 01, 2019
Title 5410 D vs. 6866 D
Sample type RNA
 
Channel 1
Source name 5410
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Rspo3++
cell type: colon cells
cell sorting: colon distal
Treatment protocol Tamoxifen (Sigma) was injected intraperitoneally into mice either as single dose or on three consecutive days (4 mg/25 g bodyweight, diluted in 200 µl corn oil) at the indicated time points to deplete Rspo3 expression
Growth protocol Animals were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.
Label Cy3
Label protocol RNA labeling was performed with the Quick-Amp Labeling Kit (Agilent Technologies) according supplier's instructions.
 
Channel 2
Source name 6866
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Rspo3 KO
cell type: colon
cell sorting: colon distal
Treatment protocol Tamoxifen (Sigma) was injected intraperitoneally into mice either as single dose or on three consecutive days (4 mg/25 g bodyweight, diluted in 200 µl corn oil) at the indicated time points to deplete Rspo3 expression
Growth protocol Animals were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.
Label Cy5
Label protocol RNA labeling was performed with the Quick-Amp Labeling Kit (Agilent Technologies) according supplier's instructions.
 
 
Hybridization protocol Whole mouse genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).
Scan protocol Scanning of microarrays was performed with 5 µm resolution and extended range (XDR) using a DNA microarray laser scanner (Agilent Technologies)
Description polarity(+)
251486841825_1_1
Data processing Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.
 
Submission date Jun 13, 2018
Last update date Jun 01, 2019
Contact name Hans-Joachim Mollenkopf
E-mail(s) [email protected]
Phone +49 30 28460 482
Organization name Max-Planck-Institute for Infection Biology
Lab Microarray/Genomics Core Facility
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL4134
Series (1)
GSE115752 R-spondin 3 regulates stem cell plasticity and recovery of damaged colon epithelium

Data table header descriptions
ID_REF
VALUE LogRatio (base 10) of Cy5/Cy3 intensities

Data table
ID_REF VALUE
1 0.09351696
2 -0.649069485
3 -1.20306683
4 -1.3815861
5 -1.316821509
6 -1.20205476
7 -0.986831488
8 -0.746272138
9 -0.288822091
10 0
11 0
12 -0.616741688
13 0
14 -0.137530976
15 -0.661947632
16 -0.486831434
17
18 0
19 0
20 0

Total number of rows: 45220

Table truncated, full table size 662 Kbytes.




Supplementary file Size Download File type/resource
GSM3188631_US22502595_251486841825_S01_GE2_1105_Oct12_1_1.txt.gz 15.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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