|
| Status |
Public on Dec 09, 2017 |
| Title |
H9_DP173PR01: Pancreatic islet sample from partially pancreatectomized patient |
| Sample type |
RNA |
| |
|
| Source name |
Pancreatic islet sample by laser capture microdissection
|
| Organism |
Homo sapiens |
| Characteristics |
age (years): 61
gender (m/f): F
body mass index (bmi): 19.433
fasting glucose (mmol/l): 4.96
diabetes status (nd (non-diabetic), t2d (type 2 diabetic), igt (impaired glucose tolerance, t3cd (type 3 diabetic)): ND
batch: 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreatic islets within resected pancreas specimens were isolated by laser capture microdissection with Zeiss Palm MicroBeam system
|
| Label |
biotin
|
| Label protocol |
10 - 25 ng total RNA was amplified using the Ovation RNA Amplification System V2 and subsequently labelled with Biotin using the Encore™ Biotin Module following the manufacturer's instructions (NuGEN Technologies, San Carlos, CA, USA).
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| |
|
| Hybridization protocol |
3.75µg cDNA per sample were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips (Affymetrix) for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix). The array was subsequently washed and stained with a fluidics station (GeneChip® Fluidics Station 450, Affymetrix) following the EukGe_WSv4_450 fluidics protocol for eukaryotic 3´-expression arrays.
|
| Scan protocol |
Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).
|
| Data processing |
Primary data analysis was performed with Affymetrix software GeneChip Operating System (GCOS) v1.4. Transcriptomic data were summarized and normalized with the Robust Multichip Analysis (RMA) using a software package (Array Studio; Omicsoft Corp., Cary, NC, USA). Batch correction of microarray data was performed using the R/Bioconductor package ComBat (Johnson et al., 2007).
Differential expression analysis comparing T2D and ND in OD or PPP cohorts:
Empirical Bayes moderated t statistics and corresponding p-values were computed using the Limma package in R correcting for age and sex covariates. P values were adjusted for multiple comparisons using the Benjamini Hochberg procedure.
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| |
|
| Submission date |
Jan 15, 2016 |
| Last update date |
Dec 09, 2017 |
| Contact name |
Mark Ibberson |
| Organization name |
SIB Swiss Institute of Bioinformatics
|
| Department |
Vital-IT
|
| Street address |
Genopode building
|
| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE76895 |
Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [partially pancreatectomized patient cohort] |
| GSE76896 |
Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients |
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