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Sample GSM1844275 Query DataSets for GSM1844275
Status Public on Oct 01, 2015
Title UPN727 cells, Crohn’s disease (CD) plasma patients 14
Sample type RNA
 
Source name UPN727 cells stimulated with CD14 Plasma
Organism Homo sapiens
Characteristics responder cell line: UPN727
diagnosis of plasma donor: Crohn’s disease (CD)
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 Crohn’s disease (CD) 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 6.25803
1053_at 6.42754
117_at 4.57704
121_at 6.29033
1255_g_at 2.07991
1294_at 6.93957
1316_at 5.40289
1320_at 2.68576
1405_i_at 11.4661
1431_at 2.46718
1438_at 4.33531
1487_at 6.67843
1494_f_at 4.25287
1552256_a_at 4.63883
1552257_a_at 5.25835
1552258_at 3.8766
1552261_at 2.8027
1552263_at 7.55483
1552264_a_at 7.17865
1552266_at 1.76826

Total number of rows: 54675

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM1844275_CD14_3-26-14_HG-U133_Plus_2_.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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