Datasets for Lyu, Hoang, and Santiago, et al. 2021
Description
Supplemental datasets 1-14 for Lyu, Hoang, and Santiago, et al. 2021. Dataset 1: Number of cells of each type identified at each developmental age using scATAC-Seq in the mouse retina. Dataset 2: Cell-type specific cis-regulatory elements and TF motifs identified in developing mouse retina. Dataset 3: Number of cells of each type identified at each developmental age using scATAC-Seq in the human retina. Dataset 4: Cell-type specific cis-regulatory elements and TF motifs identified in developing human retina. Dataset 5: Evolutionarily conserved cell-type specific cis-regulatory elements and TF motifs identified in developing retina. Dataset 6: Differentially expressed genes (DEGs) and correlated accessible chromatin regions (CARs) in stage 1-3 RPCs and Müller glia. Dataset 7: Regulatory relationships among TFs that comprise cell type-specific gene regulatory networks in stage 1-3 RPCs and Müller glia. Dataset 8: Differentially expressed genes (DEGs) and differential accessible chromatin regions (DARs) seen in RPCs and Müller glia following overexpression or knockdown of Nfia/b/x. Dataset 9: Location of Nfia/b/x ChIP-Seq peaks in P2 retina. Dataset 10: Differentially expressed genes (DEGs) and correlated accessible chromatin regions (CARs) in neurogenic RPCs and subtypes of developing retinal neurons. Dataset 11: Regulatory relationships among TFs that comprise cell type-specific gene regulatory networks in neurogenic RPCs and subtypes of developing retinal neurons. Dataset 12: List of TFs that are predicted to activate and/or repress expression of genes specific to neurogenic RPCs and subtypes of developing retinal neurons. Dataset 13: Differentially expressed genes (DEGs) observed following overexpression or knockdown of Insm1/2, listed by cell type. Dataset 14: Differentially expressed genes (DEGs) observed following overexpression or knockdown of Tcf7l1/2 or Tbx3, listed by cell type.
Files
Steps to reproduce
See STAR Methods for "Gene regulatory networks controlling temporal patterning, neurogenesis, and cell fate specification in mammalian retina" by Lyu, Hoang, and Santiago, et al. Cell Reports, in press for details. See also https://www.biorxiv.org/content/10.1101/2021.07.31.454200v1.