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Sample GSM7050212 Query DataSets for GSM7050212
Status Public on Feb 21, 2023
Title βB2-crystallin W151C knock-in Replicate 4
Sample type RNA
 
Source name βB2-crystallin W151C knock-in mouse lens
Organism Mus musculus
Characteristics age: 3 months old
tissue: lens
genotype: BetaB2-crystallin W151C knock-in
Treatment protocol BetaB2-W151C knock-in mice expressing an G to C point mutation in codon 151 of the mouse βB2-crystallin gene CRYBB2, which results in the substitution of Tryptophan 151 with Cysteine (W151C), were generated using CRISPR/Cas9 system by Shanghai Biomodel Organisms Science & Technology Development Co., Ltd. (Shanghai, China)
Extracted molecule total RNA
Extraction protocol RNA was prepared using TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. RNA was cleaned up using RNasey Mini Kit(Qiagen p/n 74104) and was quantified using a NanoDrop-1000 spectrophotometer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen p/n 74104). 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent Gene Expression hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in βB2-crystallin W151C mutant lens at 3 months old
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Feb 17, 2023
Last update date Feb 22, 2023
Contact name Wei Xiao
E-mail(s) xiaow27@mail.sysu.edu.cn
Phone 15989187341
Organization name Zhongshan Ophthalmic Center
Lab State Key Laboratory of Ophthalmology
Street address S 54 Xianlie Rd, Yuexiu District
City Guangzhou
State/province Guangdong
ZIP/Postal code 510060
Country China
 
Platform ID GPL11202
Series (1)
GSE225548 Murine lenses:βB2-crystallin W151C knock-in mice vs.wild type control mice

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 10.93415
DarkCorner 4.192041
A_55_P1989846 4.5775313
A_55_P1991598 4.3835616
A_55_P2022211 10.803524
A_55_P1980764 5.279261
A_55_P1964375 7.945604
A_51_P128876 7.1025295
A_55_P2121042 3.3084679
A_52_P219230 3.1465614
A_51_P207591 7.7439394
A_55_P2131920 8.8202
A_55_P2404223 4.6652846
A_55_P2101944 16.024675
A_52_P358860 9.583244
A_51_P119031 8.159772
A_51_P309854 2.5719457
A_51_P343900 8.734303
A_51_P234359 8.569605
A_51_P487813 8.152575

Total number of rows: 39485

Table truncated, full table size 897 Kbytes.




Supplementary file Size Download File type/resource
GSM7050212_HO3M-3.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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