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Sample GSM395765 Query DataSets for GSM395765
Status Public on May 20, 2009
Title E14.5 WT Bladder 1-6
Sample type RNA
 
Source name Bladder
Organism Mus musculus
Characteristics age: Embryonic day 14.5
tissue: Bladder
genotype: wild-type
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
 
Hybridization protocol Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Scan protocol Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Description E14.5 WT bladder
Data processing These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).


 
Submission date Apr 21, 2009
Last update date Aug 28, 2018
Contact name Amelia Soto Hopkin
E-mail(s) sotoa@uci.edu
Phone 9498249372
Organization name University of California Irvine
Department Biological Chemistry & Medicine
Lab Bogi Andersen
Street address 250 Sprague Hall
City Irvine
State/province CA
ZIP/Postal code 92617
Country USA
 
Platform ID GPL1261
Series (2)
GSE15770 WT and Get1 +/- Bladder Time Course
GSE16150 Get1 in urothelial differentiation and barrier formation
Relations
Reanalyzed by GSM1061783
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE PLIER signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 9384.88 P 4.42873e-05
AFFX-BioB-M_at 16937.3 P 4.42873e-05
AFFX-BioB-3_at 13070.4 P 4.42873e-05
AFFX-BioC-5_at 28690.3 P 4.42873e-05
AFFX-BioC-3_at 20991.1 P 4.42873e-05
AFFX-BioDn-5_at 57904.9 P 4.42873e-05
AFFX-BioDn-3_at 77711 P 4.42873e-05
AFFX-CreX-5_at 162992 P 5.16732e-05
AFFX-CreX-3_at 160167 P 4.42873e-05
AFFX-DapX-5_at 1073.56 P 4.42873e-05
AFFX-DapX-M_at 3058.13 P 6.02111e-05
AFFX-DapX-3_at 20370.9 P 4.42873e-05
AFFX-LysX-5_at 185.66 P 0.000258358
AFFX-LysX-M_at 467.906 P 0.00010954
AFFX-LysX-3_at 3915.19 P 4.42873e-05
AFFX-PheX-5_at 393.48 P 0.00010954
AFFX-PheX-M_at 1088.16 P 4.42873e-05
AFFX-PheX-3_at 4909.72 P 4.42873e-05
AFFX-ThrX-5_at 37.6909 A 0.205712
AFFX-ThrX-M_at 143.814 P 0.0151826

Total number of rows: 45101

Table truncated, full table size 1384 Kbytes.




Supplementary file Size Download File type/resource
GSM395765.CEL.gz 3.1 Mb (ftp)(http) CEL
GSM395765.CHP.gz 250.6 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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