NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1130055 Query DataSets for GSM1130055
Status Public on Apr 27, 2013
Title R26R^AC/AC (Control), biological replicate #3
Sample type RNA
 
Source name Mouse control_PSM
Organism Mus musculus
Characteristics strain background: C57BL6/6J
genotype/variation: R26R^AC/AC (Control)
developmental stage: E8.75
tissue: presomitic mesoderm (PSM)
Treatment protocol The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
Growth protocol Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
Extracted molecule total RNA
Extraction protocol The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
Label Biotin
Label protocol Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
 
Hybridization protocol Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Description Gene expression data from control PSM.
Data processing Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
 
Submission date Apr 26, 2013
Last update date Apr 27, 2013
Contact name Timothy Peter Lopez
E-mail(s) tpetelopez@gmail.com
Organization name Johns Hopkins University/Carnegie Institution
Department Biology
Lab Chen-Ming Fan
Street address 3520 San Martin Drive
City Baltimore
State/province Maryland
ZIP/Postal code 21218
Country USA
 
Platform ID GPL1261
Series (1)
GSE46426 The Presomitic Mesoderm (PSM) CREB family transcriptome

Data table header descriptions
ID_REF
VALUE MAS 5.0 Signal Intesity
DETECTION_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION_CALL DETECTION P-VALUE
1443288_at 30.14013 M 0.0561523
1429502_at 116.8314 M 0.0561523
1438257_at 82.85242 M 0.0561523
1421396_at 100.7947 P 0.0375977
1440741_at 31.66657 P 0.0107422
1445877_at 33.47486 P 0.02246094
1460013_at 182.3581 P 0.0461426
1423403_at 190.0642 P 0.0375977
1425105_at 45.15933 P 0.0461426
1430103_at 46.37772 P 0.0239258
1431198_x_at 138.4664 P 0.0375977
1436434_at 131.2375 P 0.0302734
1443109_at 48.34415 P 0.0461426
1444542_at 82.3755 P 0.0012207
1448490_at 118.1409 P 0.0185547
1418581_a_at 246.1181 P 0.0375977
1460636_at 454.2614 P 0.0302734
1435598_at 113.7203 P 0.0302734
1460727_at 342.8487 P 0.0302734
1433366_at 26.2784 P 0.0375977

Total number of rows: 19606

Table truncated, full table size 651 Kbytes.




Supplementary file Size Download File type/resource
GSM1130055_Control__3.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.