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Sample GSM938305 Query DataSets for GSM938305
Status Public on Feb 06, 2013
Title E14.5_female_gonad_Nanos3 knockout_reps1and2
Sample type RNA
 
Source name embryonic female gonad
Organism Mus musculus
Characteristics tissue: gonad
Sex: female
embryonic day: 14.5
genotype: Nanos3-/-
Treatment protocol Embryonic gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNeasy mini kit (QIAGEN, Valencia, CA) according to the manufacture's protocol.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression E14.5 mouse male gonad Nanos3 knockout
Data processing The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
All gene list of E12.5-E15.5 Nanos3-targeted female and male gonad
Averaged normalized signal intensities and flag calling for all genes of E12.5-E15.5 Nanos3-targeted female and male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).
 
Submission date May 29, 2012
Last update date Feb 06, 2013
Contact name Rie Saba
Organization name National Institute of Genetics
Department Genetic Strain Research Center
Lab Mammalian Development
Street address Yata 1111
City Mishima
State/province Shizuoka
ZIP/Postal code 411-8540
Country Japan
 
Platform ID GPL7202
Series (2)
GSE37720 Role of Nanos2 in the embryonic male gonad
GSE38297 Gene expression of mouse embryonic gonad [Nanos3]

Data table header descriptions
ID_REF
VALUE Genespring-processed signal intensity
Flag

Data table
ID_REF VALUE Flag
(-)3xSLv1 1.2218013 A
(+)E1A_r60_1 0.83373713 A
(+)E1A_r60_3 1.059413 A
(+)E1A_r60_a104 1.0602177 A
(+)E1A_r60_a107 0.8479945 A
(+)E1A_r60_a135 0.7038734 A
(+)E1A_r60_a20 0.541329 A
(+)E1A_r60_a22 0.7291265 A
(+)E1A_r60_a97 0.78013945 A
(+)E1A_r60_n11 0.7542414 A
(+)E1A_r60_n9 0.946318 A
(+)eQC-39 0.78277975 A
(+)eQC-40 1.2902778 A
(+)eQC-41 1.202587 A
(+)eQC-42 1.202587 A
A_51_P100021 1.3261855 A
A_51_P100034 1.456158 P
A_51_P100052 1.0942619 A
A_51_P100063 1.0355504 P
A_51_P100084 0.6766797 P

Total number of rows: 41267

Table truncated, full table size 1017 Kbytes.




Supplementary file Size Download File type/resource
GSM938305_E14.5_female_gonad_Nanos3_knockout_1.txt.gz 1.9 Mb (ftp)(http) TXT
GSM938305_E14.5_female_gonad_Nanos3_knockout_2.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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