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Sample GSM120232 Query DataSets for GSM120232
Status Public on Oct 17, 2006
Title TTP_KO_90ActD_BioRep1
Sample type RNA
 
Source name RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 90 minutes
Organism Mus musculus
Characteristics Cell line: Fibroblast TTP KO cell line prepared from littermate E14.5 mouse embryos, derived from parental TTP +/- male and TTP +/- female strain 129/B6; Embryo age: E14.5, Tissue: Whole embryo excluding head and organs
Biomaterial provider Mice and fibroblast derived from mice were generated in the Perry J. Blackshear lab
Treatment protocol Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS. The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 90 minutes and were extracted for RNA.
Growth protocol The fibroblasts were maintained at 37oC (5% CO2) in Dulbecco Minimal Essential Medium supplemented with 10% FBS, 2 mM L-glutamine, 100U/ml penicillin and 100 mg/ml streptomycin.
Extracted molecule total RNA
Extraction protocol The cell monolayer was rinsed twice in cold PBS, 5 ml each. Each plate of cells was then lysed in 0.6 ml of Buffer RLT (RNeasy Mini Kit, Qiagen) and total cellular RNA was prepared following the RNeasy protocol.
Label biotin
Label protocol Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.
 
Hybridization protocol 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
Scan protocol Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
Description Gene expression analysis was conducted using Mouse Genome 2.0 array (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
Data processing quantile normalization of CEL file, PDNN (PerfectMatch) estimation, log2 transformation
 
Submission date Jul 13, 2006
Last update date Aug 28, 2018
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL1261
Series (1)
GSE5324 TTP mRNA targets identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF probeset IDs from the Mouse 430 2.0 array
VALUE Quantile normalization of CEL file, PDNN probeset estimates, log2 transformation

Data table
ID_REF VALUE
1449516_a_at 8.254
1444723_at 8.414
1438307_at 8.229
1438295_at 8.302
1425589_at 8.206
1457695_at 8.536
1451182_s_at 8.559
1444989_at 8.114
1457707_at 7.976
1436061_at 7.977
1423355_at 8.914
1455461_at 8.542
1442755_at 8.473
1449045_at 9.111
1436339_at 10.009
1455739_at 8.398
1419972_at 8.773
1421121_at 8.538
1441910_x_at 8.656
1434093_at 8.577

Total number of rows: 45101

Table truncated, full table size 765 Kbytes.




Supplementary file Size Download File type/resource
GSM120232.CEL.gz 6.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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