NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM627186 Query DataSets for GSM627186
Status Public on Oct 09, 2011
Title 1138-03-A-b
Sample type RNA
 
Source name lymphocytes
Organism Homo sapiens
Characteristics scan batch: Batch 1
group: autism
subject age: 4
paternal age: 36
maternal age: 30
Extracted molecule total RNA
Extraction protocol Qiagen Qiaquick kit (Germantown, MD).
Label biotin
Label protocol Isolated total RNA was double round amplified, cleaned, and biotin-labeled using Affymetrix’s GeneChip Two-Cycle Target Labeling kit (Santa Clara, CA) with a T7 promoter and Ambion’s MEGAscript T7 High Yield Transcription kit (Austin, TX) as per manufacturer’s protocol. Amplified and labeled cRNA was quantified on a spectrophotometer and run on a 1% TAE gel to check for an evenly distributed range of transcript sizes. Twenty micrograms of cRNA was fragmented to approximately 35-200bp by alkaline treatment (200 mM Tris-acetate, pH 8.2, 500 mM KOAc, 150 mM MgOAc) and run on a 1% TAE gell to verify fragmentation. Separate hybridization cocktails were made using 15 micrograms of fragmented cRNA from each sample as per Affymetrix’s protocol.
 
Hybridization protocol Two hundred microliters (containing 10 micrograms of fragmented cRNA) of each cocktail was separately hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array for 16h at 45 degree Celsius in the Hybridization Oven 640.
Scan protocol Arrays were washed on Affymetrix’s GeneChip Fluidics Station 450 using a primary streptavidin phycoerythrin (SAPE) stain, subsequent biotinylated antibody stain, and secondary SAPE stain. Arrays were scanned on Affymetrix’s GeneChip Scanner 3000 7G with AutoLoader. Scanned images obtained by the Affymetrix GeneChip Operating Software (GCOS) v1.2 were used to extract raw signal intensity values per probe set on the array.
Data processing RMA
 
Submission date Nov 19, 2010
Last update date Oct 09, 2011
Contact name mark alter
E-mail(s) [email protected]
Organization name University of Pennsylvania
Department Center for Neurobiology and Behvior
Street address 125 S. 31st Street
City Philadelphia
State/province PA
ZIP/Postal code 19003
Country USA
 
Platform ID GPL570
Series (1)
GSE25507 Autism and increased paternal age related changes in global levels of gene expression regulation

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1007_s_at 125.5795729
1053_at 123.6999408
117_at 767.6176107
121_at 139.9942731
1255_g_at 7.276037608
1294_at 677.4356029
1316_at 35.32091961
1320_at 19.84221254
1405_i_at 2053.173742
1431_at 11.74759883
1438_at 22.57177549
1487_at 288.9051277
1494_f_at 31.92879055
1552256_a_at 78.07506715
1552257_a_at 242.6081154
1552258_at 20.48832304
1552261_at 34.91589382
1552263_at 797.8197348
1552264_a_at 747.6851141
1552266_at 7.31831239

Total number of rows: 54613

Table truncated, full table size 1210 Kbytes.




Supplementary file Size Download File type/resource
GSM627186.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap