NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM156744 Query DataSets for GSM156744
Status Public on Mar 08, 2007
Title MA-10 stably transfected with human LHR mutation Asp578Gly 3
Sample type RNA
 
Channel 1
Source name MA-10 Asp578Gly 3
Organism Mus musculus
Characteristics MA-10 stably transfected with human LHR mutation Asp578Gly
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by Trizol reagent (invitrogen).
Label Cy3
Label protocol An indirect labeling method using aminoallyl-dUTP and amino-reactive fluorescent dyes overnight.
 
Channel 2
Source name MA-10 cell
Organism Mus musculus
Characteristics MA-10 cell
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by Trizol reagent (invitrogen).
Label Cy5
Label protocol An indirect labeling method using aminoallyl-dUTP and amino-reactive fluorescent dyes overnight.
 
 
Hybridization protocol Microarrays were prehybridized in 1% bovine serum albumin, 5× SSC, 0.1% SDS for 45 min at 42°C, washed in H2O and dried by centrifugation. Cy3 and Cy5 labeled cDNA samples were mixed with 50 μl of hybridization buffer and applied to the microarrays for hybridization at 37°C for 16 hours in a hybridization chamber in the dark with gentle agitation. Slides were washed for 10 minutes at 50°C in 1× SSC and 0.1% SDS in shaking incubator, followed by a 1 minute wash in 1× SSC, three 1 minute washes in 0.1× SSC, and one rinse in H2O, at room temperature. Slides were dried by centrifugation.
Scan protocol Images were acquired for Cy3 and Cy5 channels in a 16-bit TIFF format using ScanArray Express v2.2 software. Laser power and the gain on the photomultiplier tube (PMT) were kept constant during scanning of each individual slide. The PMT setting was chosen so that the highest
intensity values lied below the saturation point. Spot intensity and background signals were quantified for each channel and used to generate spreadsheet data for Microsoft Excel.
Description cDNA from the subject (Cy3) was co-hybridized with control MA-10 cDNA labelled with (Cy5). The ratio between Cy3 and Cy5 signal was normalized and in log scale.
Data processing The acquired image was processed in ScanArray Express v2.2 software. All bad spots were flagged. Data obtained from each hybridization were stored in a database for analysis. Cy3/Cy5 ratios were normalized with respect to the median ratio value of all of the spots in the array. After normalization, spots with intensities for both channels (sum of medians) less than that of the local background were discarded. The ratios of the remaining spots were log transformed (base 2), and duplicated spots on the OncoChip were averaged to the median. Biological functions of selected genes were assigned by Gene Ontology databases.
 
Submission date Jan 18, 2007
Last update date Feb 08, 2007
Contact name TIN-LAP LEE
Organization name National Institutes of Health
Department NICHD
Lab Laboratory of Clincal Genomics
Street address 2C08 Building 49
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL4755
Series (1)
GSE6780 Evaluating the effects of activating mutations of human LH receptor in MA-10 cell

Data table header descriptions
ID_REF
VALUE Noramalized ratio for MA-10-Asp578Gly 3

Data table
ID_REF VALUE
1 -0.10159814
2 1.269033146
3 -0.01449957
4 -0.152003093
5 0.070389328
6 -0.577766999
7 -0.217591435
8 -0.029146346
9 0.163498732
10 -0.058893689
11 -0.074000581
12 -0.286304185
13 0.163498732
14 0.5360529
15 0.084064265
16 -0.395928676
17 -0.089267338
18 -0.043943348
19 0.176322773
20 -0.234465254

Total number of rows: 10159

Table truncated, full table size 169 Kbytes.




Supplementary file Size Download File type/resource
GSM156744.csv.gz 2.9 Mb (ftp)(http) CSV

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