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Sample GSM1655892 Query DataSets for GSM1655892
Status Public on Aug 09, 2016
Title FAP_081b
Sample type RNA
 
Source name Asymptomatic Male
Organism Homo sapiens
Characteristics tissue: Peripheral Whole Blood
age: 63
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX PAXgene Blood miRNA kit ( QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer. miRNAeasy kit PN 217004 (Qiagen)
Label biotin
Label protocol The cDNA generated from the WT Expression Kit is fragmented and biotin labeled with the Affymetrix GeneChip WT Terminal Labeling Kit ( Affymetrix). The cDNA is fragmented with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonucleaseI (APE I). The fragmented cDNA is then labeled with terminal deoxynucleotidyl transferase (TdT) and a biotin reagent.
 
Hybridization protocol The Gene Titan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix) is used to hybridize 3ug of the labeled cDNA to a multi peg Gene 1.1 ST Array Plate. The hybridization cocktail also contains Control Oligo B2 and 20X Eukaryotic Hybridization Controls as recommended by Affymetrix. Hybridization is carried out for 17 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). After hybridization the peg array plate is automatically washed and stained and moved to the scanner.
Scan protocol The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.
Data processing Probes to Import: Interrogating Probes and Control Probes, Probe filtering: skip, Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish
HuGene-1_1-st-v1.r4.pgf
HuGene-1_1-st-v1.r4.mps
 
Submission date Apr 12, 2015
Last update date Aug 09, 2016
Contact name Sunil Kurian
E-mail(s) smkurian@scripps.edu
Phone 858-784-7759
Organization name The Scripps Research Institute
Department Molecular and Experimental Medicine
Street address 10550 N Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL11532
Series (1)
GSE67784 A Gene Expression-based Blood Diagnostic for Symptomatic Transthyretin Amyloidosis Revealing Male and Female-specific Signatures

Data table header descriptions
ID_REF
VALUE RMA normalized signals from filtered probesets from all arrays in this study

Data table
ID_REF VALUE
7892501 4.6243
7892502 5.41968
7892503 5.45971
7892504 8.73707
7892505 3.86898
7892506 6.66876
7892507 6.48876
7892508 7.77778
7892509 9.9199
7892510 6.61687
7892511 6.07894
7892512 6.74213
7892513 5.24996
7892514 9.65092
7892515 8.57877
7892516 4.94312
7892517 7.77177
7892518 3.85802
7892519 5.30372
7892520 9.18459

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM1655892_FAP_081b.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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