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Data from: Delineating the early transcriptional specification of the mammalian trachea and esophagus

Citation

Kuwahara, Akela; Bush, Jeffrey (2020), Data from: Delineating the early transcriptional specification of the mammalian trachea and esophagus, Dryad, Dataset, https://doi.org/10.7272/Q6WW7FVB

Abstract

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.

Methods

Please see the following list for file names and descriptions

Gene expression matrices of scRNA seq in the developing foregut generated using CellRanger, aligned to mm10

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).

Nkx2.1-/- and WT bulk RNA-sequencing, aligned to mm9

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.

 

NKX2.1 ChIP-sequencing, aligned to mm9

Raw data files:

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: NKX2.1 ChIP-sequencing, raw .fastq files

 

NKX2.1 ChIP-sequencing, NKX2.1 IP DNA, replicate #1

nkx-tr_ip.bw

nkx-tr_ip.sorted.dedup.bai

nkx-tr_ip.sorted.dedup.bam

 

NKX2.1 ChIP-sequencing, NKX2.1 IP DNA, replicate #2

nkx-tr2_ip.bw

nkx-tr2_ip.sorted.dedup.bai

nkx-tr2_ip.sorted.dedup.bam

 

NKX2.1 ChIP-sequencing, input DNA, replicate #1

nkx-tr_in.bw

nkx-tr_in.sorted.dedup.bai

nkx-tr_in.sorted.dedup.bam

 

NKX2.1 ChIP-sequencing, input DNA, replicate #2

nkx-tr2_in.bw

nkx-tr2_in.sorted.dedup.bai

nkx-tr2_in.sorted.dedup.bam

 

WT trachea and esophagus epithelium, bulk RNA-sequencing, aligned to mm9

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.