|
| Status |
Public on Aug 13, 2013 |
| Title |
H1 |
| Sample type |
SRA |
| |
|
| Source name |
Hind limb skeletal muscle (soleus)
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley rats
litter: F30
diet: High Fat
weight(g): 734
mesentericfat(g): 12.4654
%bw: 1.6982833787
perirenalfat(g): 26.2102
%bw: 3.5708719346
abdominalfat(g): 13.5642
%bw: 1.8479836512
totalfat: 52.2398
%bw: 0.0711713896
heart(g): 1.4933
liver(g): 20.9179
pancreas(g): 0.9684
lkid(g): 1.9122
brain(g): 1.9792
plasmainsulin(ng/ml): 1.566
plasmainsulin(mu/l): 38.80548
glucose(mmol): 6.42
homa-ir: 11.07249696
|
| Treatment protocol |
Female breeder rats were fed either a normal fat diet (NFD, 6% soy oil, 10% sucrose w/w, 16.1 MJ/Kg digestible energy; Specialty Feeds, Glen Forest, WA) or a diet rich in saturated fat (sourced mainly from animal lard) and sucrose (HFD, 23.3% fat, 20% sucrose wt/wt, 19.6MJ/Kg digestible energy; Specialty Feeds) for the 3 weeks prior to mating and throughout pregnancy and lactation. This time period was chosen to ensure that offspring were exposed to a high fat/sucrose diet throughout the developmental period. Offspring of NFD and HFD dams were weaned at postnatal day 21 and maintained on a standard chow diet (ad libitum) for the remainder of their life. For tissue collection at 12 months, 11 male offspring (6 of control dams, 5 of high fat/sucrose-fed dams) were fasted 1 to 2 hours before being anaesthetized using inhaled isofluorane.
|
| Growth protocol |
Female Sprague-Dawley rats weighing 200 to 300g were obtained from ARC (Animal Resources Centre, WA) and housed under standard animal facility conditions (22-23°C, 30-33% humidity, 12-hour light/dark cycle). Water and food were given ad libitum.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Skeletal muscle (soleus) was collected from the hind limb of offspring and immediately snap frozen and stored at -80˚C for RNA and protein analysis. Frozen muscle (~50 mg) was homogenised with a motorized rotor-stator homogenizer (3 pulses of 15 seconds). Total RNA was extracted using RNeasy isolation kit (QIAGEN, Valencia, CA) using the manufacturer’s recommended protocol. RNA quality was determined by the MultiNA capillary electrophoresis system (Shimadzu Biotech, Sydney, NSW, Australia). Messenger RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) from 2 μg total RNA.
Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 12 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8)
36 bp reads were checked for quality using FastQC.
Reads were aligned to the Rat genome (build RN4) using BWA (aln algorithm v0.6) with default settings in Galaxy UI.
Reads aligning to exons with a mapping quality score above 20 were counted and summed over genes for each sample using HTSeq.
The resulting count matrix was tested for differential gene expression (DGE) between control and HFD offspring using the edgeR package
Genome_build: RN4
Supplementary_files_format_and_content: Count matrix
|
| |
|
| Submission date |
Aug 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark D Ziemann |
| E-mail(s) |
mark.ziemann@gmail.com
|
| Organization name |
Burnet Institute
|
| Department |
Bioinformatics Working Group
|
| Street address |
85 Commercial Rd
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3004 |
| Country |
Australia |
| |
|
| Platform ID |
GPL10669 |
| Series (1) |
| GSE49797 |
Maternal overnutrition causes insulin resistance and alters skeletal muscle oxidative phosphorylation in adult rat offspring |
|
| Relations |
| BioSample |
SAMN02315678 |
| SRA |
SRX333651 |
