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Sample GSM1844291 Query DataSets for GSM1844291
Status Public on Oct 01, 2015
Title UPN727 cells, ulcerative colitis (UC) plasma patients 08
Sample type RNA
 
Source name UPN727 cells stimulated with UC08 Plasma
Organism Homo sapiens
Characteristics responder cell line: UPN727
diagnosis of plasma donor: ulcerative colitis (UC)
Treatment protocol Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of Crohn’s disease (CD), ulcerative colitis (UC), and unrelated healthy control (uHC) plasma cultured. 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 Total RNA was extracted and amplified using an Affymetrix express cDNA synthesis kit (Affymetrix, Santa Clara, CA).
Label biotin
Label protocol cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.
 
Hybridization protocol The GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.
Scan protocol After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
Description Gene expression data from UPN727 cells stimulated with ulcerative colitis (UC) plasma
Data processing Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.
 
Submission date Aug 04, 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)
GSE71730 Plasma induced signatures reveal an extracellular milieu possessing an immunoregulatory bias in treatment naïve inflammatory bowel disease

Data table header descriptions
ID_REF
VALUE RMA normalised intensities in log2 scale

Data table
ID_REF VALUE
1007_s_at 6.59121
1053_at 6.52848
117_at 4.56474
121_at 6.30263
1255_g_at 1.87409
1294_at 6.83516
1316_at 5.43204
1320_at 2.34246
1405_i_at 10.1271
1431_at 2.36954
1438_at 3.7763
1487_at 6.40859
1494_f_at 3.92813
1552256_a_at 4.09229
1552257_a_at 5.57199
1552258_at 3.99684
1552261_at 2.74336
1552263_at 7.19919
1552264_a_at 6.86354
1552266_at 1.93608

Total number of rows: 54675

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM1844291_UC08_3-26-14_HG-U133_Plus_2_.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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