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Sample GSM1062141 Query DataSets for GSM1062141
Status Public on Jan 21, 2014
Title DMSO_24h_rep2
Sample type RNA
 
Source name J1 mESCs_DMSO_24h
Organism Mus musculus
Characteristics cell type: J1 mouse embryonic stem cells
treated with: DMSO (1μL) for 24hrs
Treatment protocol The J1 mESCs were treated with a final concentration of RA (1μM), DMSO (1μL), VC (50μg), ddH2O (1μL)
Growth protocol The J1 mESC was gelatin adapted and plated on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF at condition of 37℃ and 5% CO2.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations. Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).
Label Cy3
Label protocol Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).
 
Hybridization protocol Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.
Scan protocol Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.
Description DMSO_002
Data processing The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
 
Submission date Jan 10, 2013
Last update date Jan 21, 2014
Contact name Y Gao
E-mail(s) yyshpy@gmail.com
Organization name LVRI
Street address Xujiaping 1
City Lanzhou
ZIP/Postal code 730046
Country China
 
Platform ID GPL10787
Series (1)
GSE43405 Identifying vitamin C and RA-regulated genes in the J1 mESCs

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_30_P01017425 5.7040367
A_30_P01017426 5.9979634
A_30_P01017427 2.628827
A_30_P01017428 7.2156987
A_30_P01017429 1.1993396
A_30_P01017430 2.3682055
A_30_P01017431 2.5582151
A_30_P01017432 6.1566424
A_30_P01017433 6.3264384
A_30_P01017434 6.012678
A_30_P01017435 1.1935316
A_30_P01017436 3.8232725
A_30_P01017437 8.238889
A_30_P01017438 1.1667773
A_30_P01017439 7.6237197
A_30_P01017440 1.0382832
A_30_P01017441 3.3286943
A_30_P01017442 7.4363675
A_30_P01017443 10.971311
A_30_P01017444 2.2569127

Total number of rows: 55681

Table truncated, full table size 1287 Kbytes.




Supplementary file Size Download File type/resource
GSM1062141_DMSO_002.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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