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Sample GSM1110243 Query DataSets for GSM1110243
Status Public on Apr 01, 2013
Title PBMC_4_24
Sample type RNA
 
Source name Recipient 4; 2 Year; Non-Tolerant
Organism Homo sapiens
Characteristics recipient: 4
tissue: Peripheral Blood
time-point: 2 Year
induction: Alemtuzumab
tolerance: Non-Tolerant
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 SAPE
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.
Description 2 Year_nTOL
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
probe group file: HuGene-1_1-st-v1.r4.pgf
meta-probeset file: HuGene-1_1-st-v1.r4.mps
 
Submission date Mar 28, 2013
Last update date Apr 01, 2013
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)
GSE45593 GENOMICS TO IDENTIFY HLA IDENTICAL RENAL TRANSPLANT TOLERANCE SIGNATURES

Data table header descriptions
ID_REF
VALUE Log2 RMA normalized signal

Data table
ID_REF VALUE
7892501 1.96071
7892502 2.51051
7892503 2.07884
7892504 8.48716
7892505 2.3197
7892506 3.02516
7892507 1.71282
7892508 2.5046
7892509 6.3557
7892510 1.5147
7892511 6.44719
7892512 2.30843
7892513 1.90552
7892514 5.91536
7892515 9.33408
7892516 2.89864
7892517 1.86456
7892518 1.98402
7892519 1.93053
7892520 9.16231

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM1110243_PBMC_4_24.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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