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Sample GSM1655938 Query DataSets for GSM1655938
Status Public on Aug 09, 2016
Title FAP_200
Sample type RNA
 
Source name Symptomatic Male
Organism Homo sapiens
Characteristics tissue: Peripheral Whole Blood
age: 36
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 3.18289
7892502 5.24829
7892503 4.60296
7892504 7.98072
7892505 3.496
7892506 7.15239
7892507 6.57854
7892508 7.07385
7892509 7.90245
7892510 6.80537
7892511 5.58312
7892512 6.26105
7892513 3.99444
7892514 9.08238
7892515 8.91476
7892516 5.56738
7892517 8.16772
7892518 3.54434
7892519 5.29813
7892520 9.3306

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM1655938_FAP_200.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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