DOI: 10.7272/q6ww7fvb
title: Data from: Delineating the early transcriptional specification of the mammalian trachea and esophagus

description: The genome-scale transcriptional programs that specify the mammalian
 trachea and esophagus are unknown. Though NKX2.1 and SOX2 are hypothesized
 to be co-repressive master regulators of tracheal and esophageal fates,
 this is untested at a whole transcriptomic scale and their downstream
 networks remain unidentified. By combining single cell RNA-sequencing with
 bulk RNA-sequencing of Nkx2.1 mutants and NKX2.1 ChIP-sequencing in mouse
 embryos, we delineate the NKX2.1 transcriptional program in trachea and
 esophagus specification, and reveal a previously unknown
 NKX2.1-independent transcriptional program. To decouple regulation of the
 NKX2.1 transcriptional program from regulation by SOX2, we interrogate the
 expression of our newly-identified tracheal and esophageal markers in
 Sox2/Nkx2.1 compound mutants. Finally, we discover that NKX2.1 binds
 directly to Shh and Wnt7b and regulates their expression to control
 mesenchymal specification to cartilage and smooth muscle, coupling
 epithelial identity with mesenchymal specification. Together, these data
 create a new framework for understanding early tracheal and esophageal
 fate specification at the genome-wide level.
description: Please see the following list for file names and
 descriptions <b>Gene expression matrices of
 scRNA seq in the developing foregut generated using CellRanger, aligned to
 mm10</b> e10.5_foregut_ep.zip
 Description: FACS-purified foregut epithelium from E10.5 mouse
 embryos, single cell sequencing performed using Chromium Single Cell 3’
 Reagents Kit (10X Genomics).
 e11.5_foregut_ep.zip Description:
 FACS-purified foregut epithelium from E11.5 mouse embryos with lungs
 removed, single cell sequencing performed using Chromium Single Cell 3’
 Reagents Kit (10X Genomics).
 e11.5_lung_ep.zip Description: FACS-purified
 lung epithelium from E11.5 mouse embryos, single cell sequencing performed
 using Chromium Single Cell 3’ Reagents Kit (10X Genomics).
 <b>Nkx2.1-/- and WT bulk RNA-sequencing, aligned to
 mm9</b> wt-ep1_S30_R1_001.fastq.gz
 Description: FACS-purified foregut epithelium from WT E11.5 mouse
 embryos with lungs removed, sequenced using bulk RNA-sequencing. Replicate
 #1. wt-ep2_S31_R1_001.fastq.gz
 Description: FACS-purified foregut epithelium from WT E11.5 mouse
 embryos with lungs removed, sequenced using bulk RNA-sequencing. Replicate
 #2. wt-ep3_S32_R1_001.fastq.gz
 Description: FACS-purified foregut epithelium from WT E11.5 mouse
 embryos with lungs removed, sequenced using bulk RNA-sequencing. Replicate
 #3. Nkx2.1mut-ep1_S27_R1_001.fastq.gz
 Description: FACS-purified foregut epithelium from Nkx2.1-/-
 E11.5 mouse embryos with lungs removed, sequenced using bulk
 RNA-sequencing. Replicate #1.
 Nkx2.1mut-ep2_S28_R1_001.fastq.gz Description:
 FACS-purified foregut epithelium from Nkx2.1-/- E11.5 mouse embryos with
 lungs removed, sequenced using bulk RNA-sequencing. Replicate
 #2. Nkx2.1mut-ep3_S29_R1_001.fastq.gz
 Description: FACS-purified foregut epithelium from Nkx2.1-/-
 E11.5 mouse embryos with lungs removed, sequenced using bulk
 RNA-sequencing. Replicate #3.  
 <b>NKX2.1 ChIP-sequencing, aligned to
 mm9</b> <b>Raw data
 files:</b>
 Nkx2-1-tr2_INPUT_S70_R1_001.fastq.gz
 Nkx2-1-tr2_IP_S69_R1_001.fastq.gz
 Nkx2-1-tr_INPUT_S102_L007_R1_001.fastq.gz
 Nkx2-1-tr_IP_S101_L007_R1_001.fastq.gz
 Description:<b> </b>NKX2.1 ChIP-sequencing, raw
 .fastq files   <strong>NKX2.1
 ChIP-sequencing, NKX2.1 IP DNA, replicate #1</strong>
 nkx-tr_ip.bw
 nkx-tr_ip.sorted.dedup.bai
 nkx-tr_ip.sorted.dedup.bam  
 <strong>NKX2.1 ChIP-sequencing, NKX2.1 IP DNA, replicate
 #2</strong> nkx-tr2_ip.bw
 nkx-tr2_ip.sorted.dedup.bai
 nkx-tr2_ip.sorted.dedup.bam  
 <strong>NKX2.1 ChIP-sequencing, input DNA, replicate
 #1</strong> nkx-tr_in.bw
 nkx-tr_in.sorted.dedup.bai
 nkx-tr_in.sorted.dedup.bam  
 <strong>NKX2.1 ChIP-sequencing, input DNA, replicate
 #2</strong> nkx-tr2_in.bw
 nkx-tr2_in.sorted.dedup.bai
 nkx-tr2_in.sorted.dedup.bam  
 <b>WT trachea and esophagus epithelium, bulk
 RNA-sequencing, aligned to mm9</b>
 Es1_ep.fq.gz Description: FACS-purified
 esophagus epithelium from WT E11.5 mouse embryos, sequenced using bulk
 RNA-sequencing. Replicate #1. Es2_ep.fq.gz
 Description: FACS-purified esophagus epithelium from WT E11.5
 mouse embryos, sequenced using bulk RNA-sequencing. Replicate
 #2. Es3_ep.fq.gz Description:
 FACS-purified esophagus epithelium from WT E11.5 mouse embryos, sequenced
 using bulk RNA-sequencing. Replicate #3.
 Tr1_ep.fq.gz Description: FACS-purified
 trachea epithelium from WT E11.5 mouse embryos, sequenced using bulk
 RNA-sequencing. Replicate #1. Tr2_ep.fq.gz
 Description: FACS-purified trachea epithelium from WT E11.5 mouse
 embryos, sequenced using bulk RNA-sequencing. Replicate #2.
 Tr3_ep.fq.gz Description: FACS-purified
 trachea epithelium from WT E11.5 mouse embryos, sequenced using bulk
 RNA-sequencing. Replicate #3.