The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube

Code associated with the manuscript Zhang et al (2024).

Data availability

• GEO superseries

Data processing

1. ATAC-seq processing

Using nf-core/atacseq

nextflow run nf-core/atacseq \
	--input design.csv \
        --genome mm10 \
    	--skip_diff_analysis \
    	--min_reps_consensus 2 \
        -r 1.2.1

2. RNA-seq processing

Using nf-core/rnaseq

nextflow run nf-core/rnaseq \
        --input design.csv \
        --genome mm10 \
        --aligner star_salmon \
        --star_index false \
        --skip_biotype_qc \
    	--deseq2_vst \
        -r 3.5

3. Footprinting

Using TOBIAS nextflow pipeline

nextflow run luslab/briscoe-nf-tobias \
  -r master \
  --skip_bam_index true \
  --design design.csv \
  --genome genome.fa \
  --regions results/bwa/mergedLibrary/macs/broadPeak/consensus/consensus_peaks.mLb.clN.bed \
  --peaks results/bwa/mergedLibrary/macs/broadPeak/consensus/consensus_peaks.mLb.clN.bed \
  --blacklist ~/.nextflow/assets/nf-core/atacseq/assets/blacklists/mm10-blacklist.bed \
  --motifs motifs_archetypes.meme \
  --bd_hmem true \
  --bd_cpus 64 \

4. scATAC-seq processing

Data from : Shu et al., 2022.

module load CellRanger-ATAC/2.1.0
cellranger-atac count \
    --reference=/10x/10x_atac/refdata-cellranger-arc-mm10-2020-A-2.0.0

Code in this repo

• ATAC 1:

  • Fig 1 ATAC PCA for all cell types across time.

• ATAC 2:

  • Calculate ATAC diff accessibility for all pairwise comparisons

• ATAC 3:

  • Fig 1 ATAC space vs time quantifications
  • Fig 1 temporal heatmap

• RNA 1

  • Export normalized tables for plotting heatmaps and genes

• RNA 2a

  • Calculate RNA diff expression for all pairwise comparisons

• RNA 2b

  • Fig S1 RNAseq GO enrichment
  • Tables Supp, temporal genes for all domains, temporally dynamic and cell type specific genes

• RNA 3

  • Gene expression plot for various figures

• Footprinting 1

  • Fig 2 and Fig S1 temporal footprints and correlated TFs

• Screen

  • Fig 2 and S2: screen results and hit highlight

• Screen hits flow analysis

  • Fig S3: proportion of NFIA progenitors after PRC or Brd8 perturbation
  • Fig 5: proportion of NFIA progenitors after Nr6a1 perturbation
  • Fig 6: proportion of NFIA neurons after Nr6a1 perturbation

• Mutant RNAseq

  • Fig 3 and S3 Polycomb and Brd8 mutants: temporal and spatial patterning defects
  • Fig 4 and S4 Nr6a1 mutant: temporal defects

• Nr6a1 OE ATAC 1

  • Fig 4 Accessibility changes upon Nr6a1 overexpression

• Nr6a1 OE ATAC 2

  • Fig 4 Accessibility in wild type CaTS-ATAC for elements changing in Nr6a1 overexpression

• Time and space integration

  • Fig 5 and S5 cell type specific and temporally dynamic genes and associated elements

• NFIA/B KO ATAC

  • Fig 5 heatmap

• NIFA/B KO ATAC motif enrichment and plotting

  • Fig 5 motif enrichment plotting

• NFIA/B KO RNA

  • Fig 5 bar plots