A multi-omics digital research object for the genetics of sleep regulation

Abstract

13More and more researchers make use of multi-omics approaches to tackle complex cellular 14 and organismal systems. It has become apparent that the potential for re-use and integrate data 15 generated by different labs can enhance knowledge. However, a meaningful and efficient re-16 use of data generated by others is difficult to achieve without in depth understanding of how 17 these datasets were assembled. We therefore designed and describe in detail a digital research 18 object embedding data, documentation and analytics on mouse sleep regulation. The aim of 19 this study was to bring together electrophysiological recordings, sleep-wake behavior, 20 metabolomics, genetics, and gene regulatory data in a systems genetics model to investigate 21 sleep regulation in the BXD panel of recombinant inbred lines. We here showcase both the 22 Experiment 1 and Experiment 2 ( Figure 1) were approved by the veterinary authorities of the 95 state of Vaud, Switzerland (SCAV authorization #2534). 96 97 Animal, breeding, and housing conditions 98 34 BXD lines originating from the University of Tennessee Health Science Center (Memphis, 99 TN, United States of America) were selected for Experiment 1 and Experiment 2. These lines 100 were randomly chosen from the newly generated advanced recombinant inbred line (ARIL) 101 RwwJ panel 4 , although lines with documented poor breeding performance were not 102 considered. 4 additional BXD RI strains were chosen from the older TyJ panel for 103 reproducibility purposes and were obtained directly from the Jackson Laboratory (JAX, Bar 104Harbor, Maine). The names used for some of the BXD lines have been modified over time to 105 reflect genetic proximity. Table 1 lists the BXD line names we used in our files alongside the 106 corresponding current JAX names and IDs. In our analyses, we discarded the BXD63/RwwJ 107 line for quality reasons (see Technical Validation) as well as the 4 older BXD strains that were 108 derived from a different DBA/2 sub-strains, i.e. DBA/2Rj instead of DBA/2J for RwwJ lines 109 21 . The methods below describe the remaining 33 BXD lines, F1 and parental strains. 110 Two breeding trios per BXD strain were purchased from a local facility (EPFL-SV, Lausanne, 111 Switzerland) and bred in-house until sufficient offspring was obtained. The parental strains 112 DBA/2J (D2), C57BL6/J (B6) and their reciprocal F1 offspring (B6D2F1 [BD-F1] and 113 D2B6F1 [DB-F1]) were bred and phenotyped alongside. Suitable (age and sex) offspring was 114 transferred to our sleep-recording facility, where they were singly housed, with food and 115 water available ad libitum, at a constant temperature of 25°C and under a 12 h light/12 h dark 116 cycle (LD12:12, fluorescent lights, intensity 6.6 cds/m 2 , with ZT0 and ZT12 designating light 117 and dark onset, respectively). Male mice aged 11-14 week at the time of experiment were 118 used for phenotyping, with a mean of 12 animals per BXD line among all experiments. Note 119 that 3 BXD lines had a lower replicate number (n), with respect...

Towards mouse genetic-specific RNA-sequencing read mapping

“…Male mice from 33 BXD lines, C57BL/6J (B6), DBA/2J (D2), and F1 (Figure 1A) were either sleep-deprived (SD) for 6 hours starting at zeitgeber time (ZT) 0 (start of lights on) or not (i.e. non-sleep deprived or NSD) (Diessler et al, 2018; Jan et al, 2019). RNA was extracted from cerebral cortex and liver collected at ZT6 in both SD and NSD mice.…”