|
| Status |
Public on Nov 08, 2016 |
| Title |
liver_NASH_CL-118 |
| Sample type |
RNA |
| |
|
| Source name |
liver
|
| Organism |
Homo sapiens |
| Characteristics |
array ^sample: 8473515032_B
diagnosis: NASH
steatosis (%): 40
fibrosis (stage): 4
lobular inflammation (severity): 1
ballooning (intensity): 2
nafld activity score: 5
age (y): 63
gender: female
body mass index (kg/m2): 32.32
waist (cm): 107
aspartate transaminase (u/l): 112
alanine transaminase (u/l): 168
alkaline phosphatase (u/l): 58
triglycerides (mmol/l): 1.2
total cholesterol (mmol/l): 5.06
ldl cholesterol (mmol/l): 3.01
hdl cholesterol (mmol/l): 1.5
fasting glucose (mmol/l): 6
fasting insulin (pmol/l): 191
homa-insulin resistance: 8.49
hemoglobin a1c: 0.064
diabetes: no
liver arachidonic acid (% of total lipids): 2.60
liver eicosapentaenoic acid (% of total lipids): 0.32
liver docosahexaenoic acid (% of total lipids): 1.36
|
| 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. Nine outliers (4 NASH, 5 SS), which 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.
|
| |
|
| Submission date |
Nov 07, 2016 |
| Last update date |
Nov 08, 2016 |
| 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) |
| GSE89632 |
Genome-wide analysis of hepatic gene expression in patients with non-alcoholic fatty liver disease and in healthy donors in relation to hepatic fatty acid composition and other nutritional factors |
|
