|
| Status |
Public on Apr 17, 2019 |
| Title |
Mouse Liver Female XX 1 |
| Sample type |
RNA |
| |
|
| Source name |
Liver Female XX
|
| Organism |
Mus musculus |
| Characteristics |
age: 24-28 week old
genotype/variation: Ldlr-/-
strain: B6.129S7-Ldlrtm1Her/J
tissue: Liver
Sex: Female
sex chromosome complement: XX
rna integrity number: 9.6
|
| Treatment protocol |
24-28 week old Ldlr-/- male and female mice with an XX or XY chromosomal complement that were surgically gonadectomized at 8-12 weeks of age and then fed a Western high fat diet for 16 weeks (n = 5 female XX, n = 5 female XY, n = 4 male XX, n = 5 male XY) prior to tissue harvesting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were euthanized with ketamine/xylazine mixture (100/10 mg/ kg, injected intraperitoneally) in saline, and livers were removed in 3-4 minutes. ~100 mg of liver tissue was placed in RNA later solution (Ambion) and then RNA was extracted using Rneasy (Qiagen). Extracted RNA quality (RNA Integrity Number- RIN) was assayed by Agilent 2100 bioanalyzer. Harvested samples: N = 19; [RIN]: overall average 9.55 ± 0.05 – p > 0.29; two-way ANOVA main effect of Sex p = 0.25; main effect of chromosome p = 0.13; interaction p = 0.42, disambiguated RIN values per array are provided (see characteristics: RNA Integrity Number).
|
| Label |
biotin
|
| Label protocol |
Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0; one array per subject) according to the manufacturer’s instructions. WT cDNA Synthesis and Amplification kit and WT Sense Target Labelling and Control Reagents (Affymetrix) were used
|
| |
|
| Hybridization protocol |
Samples were hybridized with the Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0) and scanned at the UK Genomics Core Facility.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
RMA expression value derived from Partek software; transcript-level analysis
|
| Data processing |
Raw data were processed with the Expression Console (Affymetrix) and Partek for background correction, normalization, and log 2 RMA signal intensity calculation at the transcript level. Data analysis and statistical evaluations were performed with The Institute for Genomic Research (TIGR) Multi-experiment Viewer (MEV) for two-way ANOVA calculations and Excel for log 2 fold change and protected Fisher's Least Significant Difference tests. For prestatistical filtering, probesets with a log 2 signal intensity > 4.2 on at least 2/19 arrays were included. Among these, in cases where more than one probe set was annotated to the same official gene symbol, the probe set with the highest average signal intensity across all arrays was retained for statistical analysis.
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Apr 18, 2019 |
| Contact name |
Eric M Blalock |
| E-mail(s) |
[email protected]
|
| Phone |
859-323-8033
|
| Organization name |
University of Kentucky
|
| Department |
Molecular and Biomedical Pharmacology
|
| Lab |
Blalock
|
| Street address |
800 Rose St.
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40475 |
| Country |
USA |
| |
|
| Platform ID |
GPL20775 |
| Series (1) |
| GSE119497 |
XX sex chromosome complement promotes hyperlipidemia and atherosclerosis in mice |
|
