RNA-seq based analysis of gene expression in thyroids of wild-type and Keap1 knockdown mice after exposure to excess iodide.

C57BL/6J Keap1flox/flox mice were developed by Prof. Masayuki Yamamoto (DOI: 10.1016/j.bbrc.2005.10.185). These mice express lower levels of Keap1 because of the loxP site insertions (DOI: 10.1128/MCB.01591-09) and are designated as Keap1KD. 3-4 months old WT and Keap1KD mice fed a standard diet  (KLIBA NAFAG 3242, Switzerland) containing 1.5 mg/kg sodium iodine were given normal tap water with or without 0.05% sodium iodide  (Sigma, St Louis, MO, USA) for 7 days. Hence, the following groups of mice were included:

WT mice on control water (n=8)-designated as wt in the file

WT mice exposed to excess iodide (WT-IOD, n=6)- designated as wti in the file

Keap1KD mice on control water (n=8)- designated as kp in the file

 and Keap1KD mice exposed to excess iodide (Keap1KD-IOD, n=6)- designated as kpI in the file. 

 Mice were maintained in the animal facility of the Department of Physiology at  the  University  of  Lausanne  in temperature-,  light-,  and  humidity-controlled  rooms  with  a 12-hour light/dark cycle. All animal procedures were in accordance with Swiss legislature and the study was approved by the Canton of Vaud SCAV.

RNA from individual mouse thyroids was prepared as previously described (DOI: 10.1007/978-1-4939-3756-1_25) and was submitted to Alithea Genomics (Switzerland). The bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced as described previously (DOI: 10.1186/s13059-019-1671-x) to a depth of approximately 1.2 million raw reads per sample.

This research was funded by the Swiss National Science Foundation Research Grants 310030_212558,  IZCOZ0_205415 and IZCOZ0_177070