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Sample GSM1660516 Query DataSets for GSM1660516
Status Public on Oct 01, 2015
Title UPN727 cells, AIDA PL16 at baseline
Sample type RNA
 
Source name UPN727 cells stimulated with AIDA_PL16_BL serum
Organism Homo sapiens
Characteristics responder cells: UPN727 cells
patient: PL16
timepoint: at baseline
Treatment protocol Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% serum from recent-onset (RO) T1D patients that were given Placebo or Anakinra at their respective time points. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl. After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).
Growth protocol Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000.
Description Gene expression data from UPN727 cells stimulated with serum collected from patient PL16 at baseline
Data processing Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensities. Each sample was independently analyzed (5 arrays per patient, at baseline, 1, 3, 6, and 9 months into treatment, 235 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA as a statistic analysis method in Partek GS.
 
Submission date Apr 16, 2015
Last update date Oct 01, 2015
Contact name Martin Hessner
E-mail(s) mhessner@mcw.edu
Organization name Medical College of Wisconsin
Department Pediatrics
Lab Max McGee National Research Center for Juvenile Diabetes
Street address 8701 Watertown Plank Road
City Milwaukee
State/province WI
ZIP/Postal code 53226
Country USA
 
Platform ID GPL570
Series (1)
GSE37025 Interleukin-1 receptor antagonist for recent-onset type 1 diabeties mellitus: a multicenter randomized, placebo-controlled trial

Data table header descriptions
ID_REF
VALUE RMA normalized log2 Intensity.

Data table
ID_REF VALUE
1007_s_at 6.33543
1053_at 6.5574
117_at 4.38187
121_at 6.61996
1255_g_at 2.02678
1294_at 6.78425
1316_at 5.58308
1320_at 2.71515
1405_i_at 10.9426
1431_at 2.6165
1438_at 3.78314
1487_at 6.40048
1494_f_at 4.50941
1552256_a_at 4.56242
1552257_a_at 5.85061
1552258_at 4.50065
1552261_at 2.79361
1552263_at 6.71759
1552264_a_at 6.70483
1552266_at 1.62049

Total number of rows: 54675

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM1660516_41_s120_AIDA_PL16_BL_7-10-12_HG-U133_Plus_2_.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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