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Sample GSM106540 Query DataSets for GSM106540
Status Public on Apr 27, 2006
Title fibroblast_G-positive_5aza_rep2
Sample type RNA
 
Source name primary dermal fibroblasts 5aza-treated GFP-positive sorted
Organism Mus musculus
Characteristics strain: B6; gender: female; age: 0-2d; tissue: dermis; passage #: 4; treatment: 4uM 5aza; biological replicate: 2; sort: GFP-positive
Treatment protocol Freshly prepared 5-aza-2'-deoxycytidine (5A2dC) (Sigma; Saint Louis, MO, USA) stock solution was diluted in growth medium to a concentration of 4 μM. A new preparation of the drug in growth medium was added every 24 hours for a total of 48-hour drug exposure. Cells were grown in normal medium following treatment for an additional 24 hours.
Growth protocol Cultures were maintained in Dulbecco’s modified Eagle’s medium (DMEM;Invitrogen; Carlsbad, CA, USA) with L-glutamine and high glucose plus 10% FBS (Invitrogen) and 100U/mL penicillin streptomycin (Invitrogen) at 37oC and 5% CO 2. Cells were passaged at confluence by 0.25% trypsin EDTA (Invitrogen).
Extracted molecule total RNA
Extraction protocol RNeasy total RNA extraction protocol (Qiagen)
Label biotin labeled with standard Affymetrix fluorescent stain cocktail
Label protocol standard Affymetrix IVT labeling and staining protocols
 
Hybridization protocol standard Affymetrix hybridization protocol
Scan protocol standard Affymetrix scan protocol
Description X chromosome-linked GFP heterozygous female mice were used to derive dermal fibroblasts. Fibroblasts were sorted through FACS for GFP-nonexpressing cells. Cells were then untreated with 4uM 5A2dC for 48 hours followed by 24 hour recovery in normal medium. Cells were then sorted again by FACS to separate the GFP-activated (GFP-positive) and GFP-inactive (GFP-negative) cells. This sample is GFP-positive.; biological replicate 2
Data processing MAS 5.0 data processing and normalization
 
Submission date Apr 25, 2006
Last update date Apr 26, 2006
Contact name Tammy Vallender
E-mail(s) tfw@uchicago.edu
Phone 7738344065
Organization name University of Chicago
Department Human Genetics
Lab Dr. Bruce Lahn
Street address 929 E 57th St W503V
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL1261
Series (1)
GSE4718 Improved DNA methylation analysis via enrichment of demethylated cells expressing an X-inactivated GFP transgene

Data table header descriptions
ID_REF
VALUE signal generated from MAS5
ABS_CALL present / absent call

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 148.4 P
AFFX-BioB-M_at 243.5 P
AFFX-BioB-3_at 120.4 P
AFFX-BioC-5_at 335.5 P
AFFX-BioC-3_at 269.7 P
AFFX-BioDn-5_at 407.9 P
AFFX-BioDn-3_at 1474.0 P
AFFX-CreX-5_at 3267.3 P
AFFX-CreX-3_at 4581.5 P
AFFX-DapX-5_at 2.7 A
AFFX-DapX-M_at 1.0 A
AFFX-DapX-3_at 0.5 A
AFFX-LysX-5_at 0.3 A
AFFX-LysX-M_at 1.4 A
AFFX-LysX-3_at 5.2 P
AFFX-PheX-5_at 0.3 A
AFFX-PheX-M_at 0.2 A
AFFX-PheX-3_at 5.0 A
AFFX-ThrX-5_at 1.0 A
AFFX-ThrX-M_at 0.5 A

Total number of rows: 45101

Table truncated, full table size 794 Kbytes.




Supplementary data files not provided

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