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Sample GSM1655845 Query DataSets for GSM1655845
Status Public on Aug 09, 2016
Title FAP_027b
Sample type RNA
 
Source name Asymptomatic Female
Organism Homo sapiens
Characteristics tissue: Peripheral Whole Blood
age: 29
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 6.03618
7892502 5.67941
7892503 5.22964
7892504 8.83423
7892505 4.02954
7892506 6.80972
7892507 6.79703
7892508 7.90412
7892509 9.19789
7892510 6.58132
7892511 5.53015
7892512 6.72367
7892513 4.05623
7892514 10.1207
7892515 8.70476
7892516 5.49184
7892517 8.11569
7892518 5.30835
7892519 5.14274
7892520 9.20424

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM1655845_FAP_027b.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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