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Sample GSM1063891 Query DataSets for GSM1063891
Status Public on Feb 20, 2014
Title peripheral blood-T1DCase11_7
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics t1dcase/t1dcontrol pair: 11
age at sample (months): 155
time from seroconversion (months): unknown
time from t1d diagnosis (months): -3
gender: female
hla-dqb1 genotype: 02, 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 T1DCase11_7
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 3.634429077
11715101_s_at 3.998313035
11715102_x_at 3.494834812
11715103_x_at 4.349649576
11715104_s_at 3.7590742
11715105_at 2.778821126
11715106_x_at 2.965424144
11715107_s_at 5.97862601
11715108_x_at 4.24681839
11715109_at 3.866239683
11715110_at 6.148572148
11715111_s_at 4.428407503
11715112_at 3.153871537
11715113_x_at 5.601866342
11715114_x_at 5.857248113
11715115_s_at 2.177129311
11715116_s_at 3.909002086
11715117_x_at 2.366384404
11715118_s_at 2.652385032
11715119_s_at 3.231745958

Total number of rows: 49386

Table truncated, full table size 1225 Kbytes.




Supplementary file Size Download File type/resource
GSM1063891_T1DCase11_7.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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