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Sample GSM154516 Query DataSets for GSM154516
Status Public on Jan 16, 2007
Title Serum starved MEF, amplified total RNA, biological rep2
Sample type RNA
Source name 48h serum starved primary mouse embryonic fibroblasts (MEF)
Organism Mus musculus
Characteristics Genotype: C57/BLACK6, ATF1 -/+
Age: e14.5
Treatment protocol Primary mouse embryonic fibroblasts were isolated as described previously (Todaro G.J. and Green H. (1963), J. Cell Biol., 17, 299-313; Brusselbach S.U. et al. (1995), Oncogene, 10, 79-86.).
Growth protocol Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing 200µM 4-thiouridine (s4U, Sigma), 1% FBS and 1µCi 3H-cytidine (20Ci/mmol, Biotrend).
Extracted molecule total RNA
Extraction protocol RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
Label biotin
Label protocol RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
Hybridization protocol Following fragmentation, 10µg of cRNA were hybridized to MU74Av2 GeneChip (Affymetrix) according to manufacturer's instructions.
Scan protocol GeneChips were scanned using the GeneChip' Scanner 3000 7G System (Affymetrix).
Description Gene expression data from primary serum starved MEF cells grown to near confluency.
Data processing The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (10% FBS) and labelling (s4U) considered to be constant and the chip-ID as random.
Submission date Jan 10, 2007
Last update date Jan 10, 2007
Contact name Marc Kenzelmann
Phone +41 31 632 3251
Fax +41 31 632 3550
Organization name Institute of Medical Microbiology, University of Bern
Department Molecular Genome Analysis
Street address Friedbuhlstrasse 51
City Bern
ZIP/Postal code 3010
Country Switzerland
Platform ID GPL81
Series (1)
GSE6697 Expression data from spec. transcriptional activity of primary mouse embryonic fibroblasts (MEF) in response to serum.

Data table header descriptions
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
AFFX-MurIL2_at 3.2 A 0.988616
AFFX-MurIL10_at 5.3 A 0.699394
AFFX-MurIL4_at 9 A 0.39692
AFFX-MurFAS_at 109.2 P 0.003212
AFFX-BioB-5_at 106 P 0.009337
AFFX-BioB-M_at 181.4 P 0.00011
AFFX-BioB-3_at 101.4 P 0.00039
AFFX-BioC-5_at 361.1 P 0.000147
AFFX-BioC-3_at 333.9 P 7e-05
AFFX-BioDn-5_at 547.7 P 4.4e-05
AFFX-BioDn-3_at 1864.3 P 7e-05
AFFX-CreX-5_at 3746.8 P 4.4e-05
AFFX-CreX-3_at 5136 P 4.4e-05
AFFX-BioB-5_st 4.5 A 0.559354
AFFX-BioB-M_st 7.5 A 0.772364
AFFX-BioB-3_st 7.7 A 0.860518
AFFX-BioC-5_st 8.1 A 0.921998
AFFX-BioC-3_st 2.7 A 0.973889
AFFX-BioDn-5_st 6.3 A 0.559354
AFFX-BioDn-3_st 5.9 A 0.814869

Total number of rows: 12488

Table truncated, full table size 315 Kbytes.

Supplementary file Size Download File type/resource
GSM154516.cel.gz 2.8 Mb (ftp)(http) CEL

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