NGS data: Coordinated histone acetylation and methylation establish cell type-specific transcriptional programs in the mouse airway epithelium.

This dataset contains RNA sequencing (RNA-seq) data generated from Mouse Tracheal Epithelial Cells (MTECs) derived from the airway epithelium and cultured at the air–liquid interface (ALI). The experiments evaluate transcriptional changes associated with BET inhibition, Dot1l inhibition, and Pitx1 knockdown (Pitx1-KD) at different stages of differentiation. In addition, raw ChIP sequencing (ChIP-seq) data with annotated peaks of H3K27ac, H3K79me3 and Brd3 in ALI 6 are provided. In the RNA-seq files provided, the following nomenclature was used for sample annotation:"Control 4.1–4.3" correspond to untreated cells at ALI 4, whereas "Control 6.1–6.3" correspond to untreated cells at ALI 6.“DMSO” represent controls for (+)-JQ1–treated cultures named "JQ1. In these experiments, cells were exposed to (+)-JQ1 from ALI 2 to ALI 6 and harvested at ALI 6.“MOC” correspond to knockdown controls (Luc-KD) for the Pitx1-KD condition named "MOKD", at ALI 6 and ALI 14.“MOD” represent DMSO-treated controls for cultures exposed to the Dot1l inhibitor SGC0946 (named "MOSGC") from ALI 2 to ALI 6,  and harvested at ALI 6.Raw reads were pseudoaligned to Mus musculus (mm10) genome using kallisto. Counts correspond to unnormalized read numbers assigned to annotated genes and are suitable for downstream differential expression analyses.We also provide Excel files containing gene classification according to differential expression status (up-regulated, down-regulated, or non-regulated) for the experimental conditions described above. In the file named “Genes UP-DOWN-NON regulated ALI4vsALI6_JQ1vsDMSO_ALI6,” genes are categorized based on their response to (+)-JQ1 treatment and are additionally annotated according of H3K27ac binding. In the file named “Genes UP-DOWN-NON regulated_SGC0946_ALI6,” genes are categorized based on their response to SGC0946 with annotation based on H3K79me3 biding. These tables are intended to facilitate integration of transcriptional changes with chromatin features and to support comparative or enrichment analyses.