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Sample GSM3066007 Query DataSets for GSM3066007
Status Public on Sep 30, 2018
Title P0 WT 1
Sample type RNA
 
Source name XX gonads at P0 (wildtype)
Organism Mus musculus
Characteristics gender: female
tissue: ovary
sample type: mixed
developmental stage: newborn
Treatment protocol Embryonic and newborn 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.
Growth protocol Mice were housed in special pathogen free room
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted by QIAGEN (Rneasey Mini Kit) 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 (G2565BA) 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%).
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.
 
Submission date Mar 23, 2018
Last update date Sep 30, 2018
Contact name Yuzuru Kato
E-mail(s) yukato@nig.ac.jp
Phone +81-55-981-6832
Organization name National Institute of Genetics
Department Division of Mammalian Development
Lab Saga lab.
Street address 1111 Yata
City Mishima
State/province Shizuoka
ZIP/Postal code 411-8540
Country Japan
 
Platform ID GPL7202
Series (2)
GSE112275 Microarray analysis of Elavl2 knockout ovaries
GSE113305 Primordial follicle formation involves dynamic conversion of RNA regulatory proteins

Data table header descriptions
ID_REF
VALUE 75 percentile normalized signal intensity

Data table
ID_REF VALUE
A_52_P1179483 2.5675962
A_52_P18922 7.3576283
A_52_P388686 7.0914407
A_51_P449185 3.5986574
A_51_P486132 10.429731
A_52_P337092 6.520533
A_51_P462160 6.232839
A_51_P488789 9.182582
A_51_P307944 2.183415
A_52_P161987 1.7390532
A_51_P271417 2.0752168
A_52_P1180468 3.0894198
A_52_P362061 1.8056933
A_51_P474151 4.2477593
A_52_P1113 1.7315446
A_51_P319917 9.970523
A_52_P602292 5.837033
A_51_P511663 3.1021736
A_52_P122393 6.0948653
A_52_P447511 5.6969414

Total number of rows: 41175

Table truncated, full table size 906 Kbytes.




Supplementary file Size Download File type/resource
GSM3066007_SG13394341_251486840507_S001_GE1_107_Sep09_1_1.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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