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Sample GSM2252091 Query DataSets for GSM2252091
Status Public on Jul 27, 2016
Title Wildtype_control_rep1
Sample type RNA
 
Source name midbrain, adult (8-9 weeks), wildtype, MSM background
Organism Mus musculus molossinus
Characteristics tissue: midbrain
developmental stage: adult (8-9 weeks)
gender: female
strain: MSM/Ms
agouti (a) allele: wildtype
Treatment protocol The midbrain tissues were manually isolated from 8-9 weeks old mice under dissecting microscope.
Growth protocol MSM/Ms mice were derived from the colony maintained at RIKEN BioResource Center. The mutant mice for agouti (a) allele were generated by using CRISPR/Cas9 system. They were housed under controlled lighting conditions (daily light period 07:00 to 21:00).
Extracted molecule total RNA
Extraction protocol Total RNA was purified from isolated midbrain tissues with Trizol (Life technologies). The concentration of RNA was quantified using a NanoDrop-1000 spectrophotometer.
Label Cy3
Label protocol cRNA was amplified from 0.1 ug of RNA and labeled with Cy3 using Low-Input QuickAmp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy MinElute kit (QIAGEN).. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (G4852B) at 65°C for 17 h 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).
Data processing The scanned images of microarray slides were processed using Feature Extraction software version 10.5.1.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 13.1.1 (Agilent Technologies) and signal intensities were normalized by shift to 75 percentile. Baseline was set to the median of all samples. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jul 26, 2016
Last update date Jul 27, 2016
Contact name Shogo Matoba
E-mail(s) shogomatoba@gmail.com
Organization name RIKEN BioResource Research Center
Street address 3-1-1, Koyadai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-0074
Country Japan
 
Platform ID GPL21163
Series (1)
GSE84840 CRISPR/Cas9-mediated genome editing in wild-derived mice; Generation of tamed wild-derived strains by mutation of the a (nonagouti) gene

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_51_P399985 0.015624046
A_55_P2508138 0.01640606
A_55_P2805880 -0.19348192
A_55_P2419483 0.47965908
A_55_P2739683 -0.14686108
A_51_P211903 -0.08058739
A_66_P121325 0.042254925
A_51_P226429 0.10756445
A_55_P2841743 0.018859863
A_55_P2737159 0.12397909
A_55_P2728466 -0.08392763
A_55_P2101526 0.14756298
A_52_P1132414 0.5096283
A_66_P135936 -0.10800266
A_55_P2805396 -0.21601105
A_55_P2717104 -0.21968842
A_55_P2909714 0.02336073
A_55_P2744310 0.008089542
A_52_P83363 -0.20113945
A_55_P2091691 -0.13036823

Total number of rows: 56743

Table truncated, full table size 1390 Kbytes.




Supplementary file Size Download File type/resource
GSM2252091_WT1.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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