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Sample GSM1024390 Query DataSets for GSM1024390
Status Public on Jun 26, 2013
Title vector 1
Sample type RNA
 
Source name 4T1 vector transduced
Organism Mus musculus
Characteristics strain: BALB/cfC3H
cell line: 4T1
genotype/variation: Control
Growth protocol Vector and Wnt5a expressing 4T1 cells were passaged and grown according to ATCC standard instructions for 4T1 cells. When cells were 70% confluent RNA was extracted.
Extracted molecule total RNA
Extraction protocol RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Label biotin
Label protocol Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
 
Hybridization protocol The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Scan protocol Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Data processing The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used.
 
Submission date Oct 23, 2012
Last update date Jun 26, 2013
Contact name Rosa Serra
E-mail(s) rserra@uab.edu
Phone 205-934-0842
Organization name University of Alabama at Birmingham
Department Cell Biology
Lab Serra
Street address 1918 University Blvd. 660 MCLM
City Birmingham
State/province AL
ZIP/Postal code 35294-0005
Country USA
 
Platform ID GPL6246
Series (2)
GSE41791 Differential expression in Wn5a and vector transduced 4T1 cells. [Affymetrix microarray data]
GSE41793 Differential expression in Wn5a and vector transduced 4T1 cells.

Data table header descriptions
ID_REF
VALUE log2 RMA signal intensity

Data table
ID_REF VALUE
10344614 -0.19509935
10344616 -0.029899597
10344618 -0.013785839
10344620 -0.019331932
10344622 0.15326071
10344624 -0.27955246
10344633 -0.012295723
10344637 0.037216187
10344653 -0.003151894
10344658 0.012822628
10344674 -0.00111723
10344679 -0.030760765
10344705 -0.11953926
10344707 0.047767162
10344713 -0.51821995
10344715 0.006736755
10344717 -0.38842106
10344719 -0.03083849
10344721 0.010615349
10344723 -0.85358095

Total number of rows: 28853

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1024390_MWV-1_MoGene-1_0-st-v1_.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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