NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1005588 Query DataSets for GSM1005588
Status Public on Jan 01, 2013
Title DMSO_24h_rep2
Sample type RNA
 
Source name J1 mESC, DMSO, 24h, replicate 2
Organism Mus musculus
Characteristics strain: 129S4/SvJae
tissue: Inner Cell Mass
cell type: Embryonic Stem Cell
treatment: 24h in DMSO
Treatment protocol J1 mESCs maintained in medium containing 1000 U/mL LIF and treated by 3 μΜ CHIR99021 or 1mM AICAR for 24h.
Growth protocol The J1 mouse embryonic stem cell line purchased from ATCC (Manassas, VA, USA) was gelatin adapted and grown 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 (ESGRO, Millipore, USA).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
Label Cy3
Label protocol Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).
 
Hybridization protocol Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.
Scan protocol Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.
Description Gene expression after 24h in DMSO(control) treated J1 mESCs
Data processing 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 Sep 18, 2012
Last update date Jan 01, 2013
Contact name Yongyan Wu
E-mail(s) wu-yongyan@163.com
Organization name Shanxi Medical University
Department Department of Otolaryngology Head & Neck Surgery, The First Hospital
Lab Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer
Street address No.85 South Jiefang Road, Taiyuan, Shanxi, China
City Taiyuan
State/province Shanxi
ZIP/Postal code 030001
Country China
 
Platform ID GPL10787
Series (1)
GSE40959 Identifying CHIR99021 and AICAR-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
GSM1005588_DMSO_002.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap