Dataset for "The Impact of Physical Inactivity, Ageing, and Nutrition on Adipose Tissue Function"

These files contain the raw expression (in FPKM) data from RNA sequencing data sets generated from adipose tissue samples collected before and at the end of a long-term head-down tilt bed rest study in healthy young males (ref: AO-13-BR). These files are also RNA sequencing data sets generated from adipose tissue and skeletal muscle samples collected from healthy young and older adults in a cross-sectional study (ref: 16/SW/0003).

Subjects:
Omic sciences and technologies

Cite this dataset as:
Trim, W., Walhin, J., Koumanov, F., Lindsay, M., Bouloumié, A., Turner, J., Thompson, D., 2019. Dataset for "The Impact of Physical Inactivity, Ageing, and Nutrition on Adipose Tissue Function". Bath: University of Bath Research Data Archive. Available from: https://doi.org/10.15125/BATH-00692.

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Access on request: Data are available on request prior to the point of publication of these data, after the submission of the PhD thesis they are in reference to.

Creators

Will Trim
University of Bath

Jean-Philippe Walhin
University of Bath

Mark Lindsay
University of Bath

Anne Bouloumié
Institute of Cardiovascular and Metabolic Diseases (I2MC)

James Turner
University of Bath

Dylan Thompson
University of Bath

Contributors

University of Bath
Rights Holder

Documentation

Data collection method:

Adipose tissue samples were collected under local anaesthesia from abdominal subcutaneous adipose tissue depots, 5cm lateral to the umbilicus by needle aspiration. Skeletal muscle samples were collected from the Vastus lateralis using the Bergstrom biopsy technique . All samples were collected following an overnight fast in the rested state. Samples were briefly cleaned of visible signs of blood, weighed and immediately snap frozen in liquid nitrogen and stored at -80 degrees until analysis. Tissue samples were thawed and digested in QUIzol reagent, to extract RNA fractions. RNA was DNase treated and QC'd to assess sample quantity and quality. Samples at a set concentration were sent for next-generation sequencing at the Wellcome Trust Oxford Genomics Centre on a HiSeq4000 Illumina instrument, Deoxynucleotide triphosphate (dUTP) was incorporated into the second strand, to facilitate selective degradation of dUTP-tagged cDNA to generate a cDNA library suitable for sequencing. cDNA was end-repaired, A-tailed, and adapter-ligated. Samples also underwent uridine digestion. Prepared libraries were size-selected, multiplexed across 8 lanes, and quality controlled before paired end sequencing over 12 lanes of a flow cell. FastQ sequencing files were uploaded to the Galaxy web platform (usegalaxy.org) for quality control analysis. Raw sequencing files were splice-aligned to the GRCh38/hg38 reference genome using Hisat2 with a mapping distance <500 kb between reads. Genome annotation was performed using Ensembl against the reference genome. Expression levels (fragments per kilobase of transcript per million mapped reads (FPKM]) were estimated using Stringtie.

Technical details and requirements:

Equipment and software used: - 14G adipose biopsy needle and 10 or 50mL syringe - Bergstrom biopsy needle. - Quizol reagent. - DNase I and DNase buffer (Qiagen) - RNase/DNase free water - Phenol-Chloroform-Isoamyl alcohol 25:24:1 - Tris EDTA - Sodium acetate - nucleotide free water - Qubit - SpectroStar Nano - Agilent tapestation 4200 - usegalaxy.org - Hisat2 - Ensembl - Stringtie

Funders

Biotechnology and Biological Sciences Research Council (BBSRC)
https://doi.org/10.13039/501100000268

Targeting Bed Reset-Induced Adipose Tissue Dysfunction with Anti-Inflammatory and Antioxidant Nutrients
BB/N004809/1

Publication details

Publication date: 1 November 2019
by: University of Bath

Version: 1

DOI: https://doi.org/10.15125/BATH-00692

URL for this record: https://researchdata.bath.ac.uk/id/eprint/692

Contact information

Please contact the Research Data Service in the first instance for all matters concerning this item.

Contact person: Will Trim

Departments:

Faculty of Humanities & Social Sciences
Health

Research Centres & Institutes
Milner Centre for Evolution