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Sample GSM4475968 Query DataSets for GSM4475968
Status Public on Apr 02, 2021
Title Patient 9 Peripheral blood mononuclear cells placebo
Sample type RNA
 
Source name Peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics age: 40
gender: F
treatment: placebo
Treatment protocol The study was a single-center, single-blind, randomized, two-period/crossover clinical trial.Men and women with Addison’s disease for > 12 months on stable cortisol replacement (with HC 15 to 30 mg/day) for ≥ 3 months were eligible for inclusion. Other inclusion criteria were age 20 to 60 years, body mass index 20 to 30 kg/m2, and ability to comply with the protocol procedures. Exclusion criteria were GC replacement therapy for indication other than Addison’s disease, any treatment with sex hormones including contraceptive drugs, treatment with levothyroxine, renal or hepatic failure, significant and symptomatic cardiovascular disease, diabetes mellitus, current infectious disease with fever, and pregnancy or breastfeeding. HC infusion was prepared by adding 0.4 mL of Solu-Cortef® 50 mg/mL to 999.6 mL 0.9% saline, which resulted in 1 mg HC per 50 mL intravenous infusion. HC infusion was adjusted in accordance with previous observations in healthy males and interventions in both sexes. The aim was to achieve a near-physiological circadian cortisol curve with early morning rise in serum cortisol that would peak at 7 AM and trough concentrations at midnight. In the GC-withdrawal intervention, 0.9% saline infusion alone was administered using the same volume as during the HC infusion. Thus, a person weighing 75 kg received 2 L of intravenous infusion over 26 hours during each intervention.
Extracted molecule total RNA
Extraction protocol PBMCs were isolated on-site from whole blood using a gradient-based separation procedure and Ficoll-Paque PREMIUM (GE Healthcare). Purified PBMCs were lysed using QIAzol Lysis Buffer (Qiagen, Hilden, Germany) on a QIAshredder column (Qiagen). The lysate was subsequently frozen and stored at –70°C. Samples were eluted in RNAse-free water. RNA concentration was measured spectrophotometrically and the A260/A280 ratio was 1.97 to 2.05.
Label biotin
Label protocol Microarray gene expression analysis in both PBMC and adipose tissue was performed at the Array and Analysis Facility, Science for Life Laboratory at Uppsala Biomedical Center (BMC), Sweden. RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc., Palo Alto, CA). Total RNA 150 ng from each PBMC sample and 10 ng from each adipose tissue sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 1, Affymetrix Inc., Santa Clara, CA).
 
Hybridization protocol GeneChip® ST Arrays (GeneChip® Human Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (P/N 702731 Rev. 3, Affymetrix Inc.), the arrays were then washed and stained using the GeneChip™ Fluidics Station 450
Scan protocol Scanned using the GeneChip® Scanner 3000 7G
Description -
Data processing Gene level summary of the exon array was performed after RMA data processing using quality control of transcriptomic data within Qlucore Omics Explorer 3.3 Principal component analysis (PCA) with cross validation and data consistency was used to confirm data consistency. Differential gene expression was determined by a paired t-test comparing the two interventions. Principal component analysis (PCA) was performed to provide further quality control and to define the relationship of variance between samples, allowing structure within the data set to be defined (Qlucore Omics Explorer 3.3, Lund, Sweden).
HuGene-2_0-st.pgf
HuGene-2_0-st-v1.na36.hg19.transcript.csv
 
Submission date Apr 14, 2020
Last update date Apr 03, 2021
Contact name Adam Stevens
E-mail(s) adam.stevens@manchester.ac.uk
Phone 44 161 701 6907
Organization name University of Manchester
Department Medicine
Street address Oxford Road
City Manchester
ZIP/Postal code M13 9PT
Country United Kingdom
 
Platform ID GPL16686
Series (2)
GSE148639 Identification of human glucocorticoid response markers using integrated multi-omic analysis [Peripheral blood mononuclear cells]
GSE148642 Identification of human glucocorticoid response markers using integrated multi-omic analysis

Data table header descriptions
ID_REF
VALUE RMA signal estimates from Qlucore 3.5 normalised for individual (i.e. paired data).

Data table
ID_REF VALUE
16821541 -0.66055
16669796 -0.234
17113147 -0.357
16757160 -0.29805
16763410 0.2624
17061210 0.12005
16762126 0.13755
17021478 -0.126451
16705961 -0.5252
16889807 0.240251
16923179 0.24925
16775386 0.3468
16782026 0.2529
16663033 -0.25225
16760928 -0.3703
16976211 -0.129951
16836311 0.2668
16984287 -0.09975
16989202 0.235299
17106067 0.15545

Total number of rows: 53617

Table truncated, full table size 942 Kbytes.




Supplementary file Size Download File type/resource
GSM4475968_PA259_09-145_160623_HuGene-2_0-st_.CEL.gz 7.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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