Data from: Delineating the early transcriptional specification of the mammalian trachea and esophagus
Cite this dataset
Kuwahara, Akela; Bush, Jeffrey (2020). Data from: Delineating the early transcriptional specification of the mammalian trachea and esophagus [Dataset]. Dryad. 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.