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Data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223917

Liu, Zhiyuan, Yujie Chen, Qimin Xia, Menghan Liu, Heming Xu, Yi Chi, Yujing Deng, and Dong Xing. “Linking Genome Structures to Functions by Simultaneous Single-Cell Hi-C and RNA-Seq.” Science 380, no. 6649 (June 9, 2023): 1070–76. https://doi.org/10.1126/science.adg3797.

wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/soft/GSE223917_family.soft.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/miniml/GSE223917_family.xml.tgz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/matrix/GSE223917_series_matrix.txt.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_RAW.tar
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_HiRES_brain.rna.umicount.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_HiRES_brain_metadata.xlsx
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_HiRES_emb.rna.umicount.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_HiRES_emb_GADIs.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_HiRES_emb_metadata.xlsx
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_HiRES_emb_residuals-updated-02-22-2023.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_HiRES_emb_significant_DIs.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_brain_genome1.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_brain_genome2.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_embryo_genome1.tsv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE223nnn/GSE223917/suppl/GSE223917_embryo_genome2.tsv.gz

  • gene expression, allele-specific

    • GSE223917_embryo_genome1.tsv.gz, GSE223917_embryo_genome2.tsv.gz
    • GSE223917_brain_genome1.tsv.gz, GSE223917_brain_genome2.tsv.gz

  • scHi-C, 20kb resolution

    • GSE223917_RAW - lots of files like GSM6998595_GasaE751001.pairs.gz (pairs format) and GSM6998595_GasaE751001.20k.0.clean.3dg.txt.gz (not sure)

  • Cell IDs vs. metadata. Metadata includes "Cell type"

    • GSE223917_HiRES_brain_metadata.xlsx 20 Ast - astrocytes 204 Ex1 - excitatory neuron cluster 1 43 Ex2 13 Ex3 52 In1 - inhibitory neuron cluster 1 47 In2 20 Oli - oligodendrocytes
    • GSE223917_HiRES_emb_metadata.xlsx 387 ExE ectoderm 485 ExE endoderm 304 ExE mesoderm 128 NMP 701 blood 447 early mesenchyme 413 early mesoderm 476 early neurons 139 endoderm 221 epiblast and PS 304 epithelial cells 340 intermediate mesoderm 563 mitosis 953 mix late mesenchyme 67 myocytes 454 neural ectoderm 227 neural tube 137 notochord 180 oligodendrocytes and progenitors 473 radial glias 70 schwann cell precursors

  • Differential interactions

    • GSE223917_HiRES_emb_significant_DIs.tsv.gz 151513 early_mesenchyme 444692 early_mesoderm 1416102 early_neurons 51898 endoderm 360132 epiblast_and_PS 98065 epithelial_cells 217127 ExE_mesoderm 176388 intermediate_mesoderm 1335808 mix_late_mesenchyme 13926 myocytes 748130 neural_ectoderm 66632 neural_tube 24201 NMP 33558 notochord 96461 oligodendrocytes_and_progenitors 454679 radial_glias 481 schwann_cell_precursors

  • Using the embryonic top DIs and gene expression profiles, we identified 390,252 significant DI-gene associations (FDR <1%), involving 1955 genes and 223,607 DIs, which we refer to as gene-associated DIs (GADIs)

    • GSE223917_HiRES_emb_GADIs.tsv.gz
    • GSE223917_HiRES_emb_residuals-updated-02-22-2023.tsv.gz - We then calculated a “residual” for each GADI-gene pair, defined as the difference of the GADI interaction strength and the expression level from the same metacell, similarly as in the “chromatin potential” approach (44), and performed a one- sample t test using all metacells along the trajectory to determine whether the residual was significantly deviated from zero