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Sample GSM1063768 Query DataSets for GSM1063768
Status Public on Feb 20, 2014
Title peripheral blood-T1DCase3_1
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics t1dcase/t1dcontrol pair: 3
age at sample (months): 75
time from seroconversion (months): 59
time from t1d diagnosis (months): -9
gender: female
hla-dqb1 genotype: 0302
Growth protocol 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70C until analyzed.
Extracted molecule total RNA
Extraction protocol Total whole-blood RNA was extracted from the samples using PAX gene RNA Blood RNA kit (Qiagen, Germany) according to manufacturer's instructions. RNA quality and quantity was determined using Nano Drop ND-1000 (Nano Drop Technologies, USA) and Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).
Label biotin
Label protocol 50 ng of total RNA was processed to cDNA with Nugen Ovation RNA Amplification System V2 (cat. no 3100-60) and subsequently biotin-labelled and fragmented with Nugen Encore Biotin Module (cat. no 4200-A01) according to manufacture’s protocol.
 
Hybridization protocol Samples were hybridized to GeneChip Human Genome U219 array plate with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (cat. no 901530).
Scan protocol GeneTitan MC Instrument was used to hybridize, wash, stain and scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control GeneTitan hybridization process and in summarizing probe cell intensity data (.CEL file generation).
Description T1DCase3_1
Data processing Sample T1DControl7_4 was excluded from the final analysis as an outlier. The CEL file and a readme for T1DControl7_4 containing the Metadata are provided as supplementary files on the Series record. The intensities were RMA normalized and log2-transformed using R/Bioconductor.
 
Submission date Jan 14, 2013
Last update date Feb 20, 2014
Contact name Henna Kallionpää
E-mail(s) henna.kallionpaa@btk.fi
Phone +358-2-333-8001
Organization name University of Turku
Department Turku Centre for Biotechnology
Lab Riitta Lahesmaa
Street address P.O. Box 123
City Turku
ZIP/Postal code FIN-20521
Country Finland
 
Platform ID GPL13667
Series (2)
GSE30211 Gene expression changes during Type 1 diabetes pathogenesis
GSE43488 Genome-wide expression kinetics of children with Type 1 diabetes (T1D) -associated autoantibodies or progression towards clinical T1D, compared to healthy matched controls .

Data table header descriptions
ID_REF
VALUE RMA-normalized and log2 transformed.

Data table
ID_REF VALUE
11715100_at 3.53751975
11715101_s_at 4.18675705
11715102_x_at 3.428221506
11715103_x_at 4.052900929
11715104_s_at 3.411520199
11715105_at 2.634561953
11715106_x_at 4.263902482
11715107_s_at 5.960573006
11715108_x_at 4.529031152
11715109_at 4.039439934
11715110_at 5.508077125
11715111_s_at 3.508788329
11715112_at 3.190685607
11715113_x_at 5.848063884
11715114_x_at 5.613056096
11715115_s_at 2.400602952
11715116_s_at 3.992231423
11715117_x_at 3.261595874
11715118_s_at 2.362128137
11715119_s_at 3.564638235

Total number of rows: 49386

Table truncated, full table size 1226 Kbytes.




Supplementary file Size Download File type/resource
GSM1063768_T1DCase3_1.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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