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Sample GSM5211987 Query DataSets for GSM5211987
Status Public on Jan 04, 2022
Title E18.5 ureters, Rbpj-cKO vs control, rep2
Sample type RNA
 
Channel 1
Source name control
Organism Mus musculus
Characteristics strain: NMRI
genotype: Rbpj(fl/?)
gender: female
developmental stage: E18.5
tissue: ureter
Treatment protocol Ureters were mechanically dissected from E18.5 embryos.
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.
Label AlexaFluor647
Label protocol Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Life Technologies) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and that reaction volumes were halved.
 
Channel 2
Source name Rbpj-cKO
Organism Mus musculus
Characteristics strain: NMRI
genotype: Tbx18(cre/+);Rbpj(fl/fl)
gender: female
developmental stage: E18.5
tissue: ureter
Treatment protocol Ureters were mechanically dissected from E18.5 embryos.
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.
Label AlexaFluor555
Label protocol Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Life Technologies) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and that reaction volumes were halved.
 
 
Hybridization protocol cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies).
Scan protocol Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).
Data processing Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE2_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of ProcessedSignal (PS) values (for each channel independently) to retrieve one resulting value per non-control probe, sample, and channel. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5. For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula: normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i) Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.
 
Submission date Mar 25, 2021
Last update date Jan 04, 2022
Contact name Andreas Kispert
E-mail(s) kispert.andreas@mh-hannover.de
Phone 0049 5115324017
Organization name Medizinische Hochschule Hannover
Department Molekularbiologie
Lab Kispert
Street address Carl-Neuberg-Str. 1
City Hannover
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL11202
Series (1)
GSE169662 Transcripts identified by microarray analysis that were deregulated in E18.5 Tbx18(cre/+);Rbpj(fl/fl) (Rbpj-cKO) ureters

Data table header descriptions
ID_REF
VALUE Fold change values always represent Rbpj-cKO / control. Measurements of control features were removed.

Data table
ID_REF VALUE
A_51_P100034 -1.079187345
A_51_P100174 1.242156729
A_51_P100208 -2.412725316
A_51_P100289 1.065992223
A_51_P100298 1.042310709
A_51_P100309 1
A_51_P100327 1.242112498
A_51_P100347 1
A_51_P100519 1
A_51_P100537 1
A_51_P100573 -1.122149309
A_51_P100624 1.011523829
A_51_P100625 1.171776522
A_51_P100768 1
A_51_P100776 1
A_51_P100787 -1.008139333
A_51_P100828 1.11921896
A_51_P100852 1.144607981
A_51_P100991 1.16154624
A_51_P100997 1.001200312

Total number of rows: 39429

Table truncated, full table size 878 Kbytes.




Supplementary file Size Download File type/resource
GSM5211987_M5170.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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