|
| Status |
Public on Sep 30, 2019 |
| Title |
liver_CL-122-BL |
| Sample type |
RNA |
| |
|
| Source name |
liver
|
| Organism |
Homo sapiens |
| Characteristics |
array ^sample: 3998675021_J
time point: baseline
diagnosis: NASH
steatosis (%): 40
fibrosis (stage): 3
lobular inflammation (severity): 1
ballooning (intensity): 2
nafld activity score: 5
age (y): 35
gender: 0
body mass index (kg/m2): 36.29
waist (cm): 123.50
aspartate transaminase (u/l): 32
alanine transaminase (u/l): 36
alkaline phosphatase (u/l): 73
triglycerides (mmol/l): 1.73
total cholesterol (mmol/l): 4.25
ldl cholesterol (mmol/l): 2.38
hdl cholesterol (mmol/l): 1.08
fasting glucose (mmol/l): 7.9
fasting insulin (pmol/l): 127
homa-insulin resistance: 7.43
hemoglobin a1c: 0.08
diabetes: 1
erythrocyte arachidonic acid (% of total lipids): 12.77
erythrocyte eicosapentaenoic acid (% of total lipids): 0.39
erythrocyte docosahexaenoic acid (% of total lipids): 3.91
liver arachidonic acid (% of total lipids): 2.44
liver eicosapentaenoic acid (% of total lipids): 13.20
liver docosahexaenoic acid (% of total lipids): 1.05
liver arachidonic acid (% of diacylglycerols): 0.35
liver eicosapentaenoic acid (% of diacylglycerols): 0.41
liver docosahexaenoic acid (% of diacylglycerols): 0.31
liver arachidonic acid (% of phospholipids): 11.73
liver eicosapentaenoic acid (% of phospholipids): 0.45
liver docosahexaenoic acid (% of phospholipids): 5.33
liver arachidonic acid (% of triacylglycerols): 0.22
liver eicosapentaenoic acid (% of triacylglycerols): 0.00
liver docosahexaenoic acid (% of triacylglycerols): 0.06
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from liver biopsies using the mirVana miRNA Isolation kit (Life Technologies Corp., Carlsbad, CA, USA). RNA concentration and purity were assessed with a Thermo Scientific's NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
200 ng of RNA were labelled and amplified following Illumina Whole Genome Expression - DASL assay kit for partially degraded and FFPE derived RNA.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Data processing |
Data was checked for overall quality using R (v2.15.1) with the lumi Bioconductor package. Two samples (1 baseline, 1 at 12 months) that fell below the threshold for one or more of the quality metrics calculated with this package, were excluded from further analysis. The data were imported in GeneSpring v12.5 (Agilent) and normalized using a quantile normalization followed by a “per probe” median centered normalization (for visualization).
|
| |
|
| Submission date |
Mar 23, 2017 |
| Last update date |
Sep 30, 2019 |
| Contact name |
Johane P. Allard |
| E-mail(s) |
johane.allard@uhn.on.ca
|
| Phone |
416-340-5159
|
| Organization name |
University Health Network
|
| Department |
Medicine
|
| Street address |
585 University Ave, 9-NU-973
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 2N2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL14951 |
| Series (1) |
| GSE96971 |
Genome-wide analysis of hepatic gene expression in patients with non-alcoholic steatohepatitis (NASH) before and after 1 year supplementation with n-3 polyunsaturated fatty acids (PUFA) from fishoil |
|
