Table 2.

Omic Methods Discussed in this Paper and in Salhadar et al.(18)

Modality	Method	Description	Application in Current Paper
Protein mass spectrometry	Quantitative comprehensive proteomics (SILAC)	Stable isotope-based metabolic labeling used to quantify abundance of every expressed protein in cultured cells	Identification of effects of vasopressin and PKA deletion on proteome of collecting duct cells
	Quantitative comprehensive proteomics (TMT)	Multiplexed chemical labeling of tryptic peptides to quantify abundance of every expressed protein in cell or tissue	Identification of effects of vasopressin on proteome of native collecting ducts
	Dynamic SILAC	Pulse labeling of proteins with stable isotopes to measure half-lives and translation rates proteome-wide	Identification of effects of vasopressin on proteome of collecting duct cells
	Quantitative phospho-proteomics	Proteome-wide SILAC or TMT quantification of tryptic peptides followed by phosphopeptide enrichment using affinity chromatography	Identification of effects of vasopressin or PKA deletion on phosphoproteome in collecting duct
Next generation sequencing (NGS)	RNA-seq	Detection and quantification of all mRNA species and non-coding RNAs	Identification of effects of vasopressin or PKA deletion on transcriptome in collecting duct
	ChIP-seq for RNA polymerase II	Chromatin immunoprecipitation using antibody to RNA Polymerase II followed by NGS to mark active cis-regulatory elements and identify transcribed genes	Genome-wide identification of actively transcribed genes in collecting duct cells
	ChIP-seq for histone H3K27 acetylation	Chromatin immunoprecipitation using antibody to histone H3 acetylated at lysine 27 followed by NGS to mark active cis-regulatory elements	Genome-wide identification of effects of vasopressin on enhancer activity
	ATAC-seq	Tn5 transposase insertion of sequencing adapters into open chromatin regions of the genome followed by NGS	Genome-wide identification of effects of vasopressin on DNA accessibility
	ChIP-seq for individual transcription factors	Chromatin immunoprecipitation using antibody to transcription factor proteins followed by NGS to identify binding sites occupied by the transcription factor	Genome-wide identification of binding sites for CREB and C/EBPβ in collecting duct cells