Data CitationsMurphy DP, Hughes AE, Lawrence KA, Myers CA, Corbo JC

Data CitationsMurphy DP, Hughes AE, Lawrence KA, Myers CA, Corbo JC. genes, which are sorted by least expensive modified p-value. (A-H) Genes enriched in OFF bipolar cells. (I-O) Genes enriched in ON bipolar cells. nTrans?=?mean quantity of transcripts expressed per cell in each cluster identified as a bipolar cell type. PercExpr?=?percentage of cells within each cluster found out to express the indicated gene. elife-48216-fig2-data1.pdf (679K) DOI:?10.7554/eLife.48216.008 Figure 6source data 1: Additional images of reporter injections. Additional replicates from in vivo subretinal injection and electroporation of reporter pairs demonstrated in Number 6C. Schematics of each reporter pair are demonstrated at the right of each panel, with WT (black), inactivated K50 (crossed out), and novel Q50 (yellow) motif sites demonstrated as ellipses. elife-48216-fig6-data1.pdf (23M) DOI:?10.7554/eLife.48216.017 Supplementary file 1: Biological replicate and sequencing metrics for ATAC-seq and RNA-seq. Uncooked sequencing reads are the quantity of combined reads for each sample. Processed reads are those reads remaining after filtering out those that are improperly combined, possess poor mapping quality, align to the mitochondrial genome, align to ENCODE blacklisted areas, or arise from PCR duplicates. RIN?=?RNA integrity quantity. elife-48216-supp1.xlsx (12K) DOI:?10.7554/eLife.48216.019 Supplementary file 2: Primers used in this work. Primers used in creation of promoter constructs and in RT-qPCR experiments are outlined. elife-48216-supp2.xlsx (12K) DOI:?10.7554/eLife.48216.020 Supplementary file 3: Datasets and accessions. elife-48216-supp3.xlsx (12K) DOI:?10.7554/eLife.48216.021 Supplementary file 4: Annotated ATAC-seq peaks and counts. Raw count data for those NHS-Biotin ATAC-seq peaks recognized in photoreceptor and bipolar cell populations. Peaks recognized in individual replicates from each cell type are demonstrated on separate bedding. elife-48216-supp4.xlsx (52M) DOI:?10.7554/eLife.48216.022 Supplementary file 5: Differentially expressed genes. Genes identified as differentially indicated between aggregate bipolar cells and either pole or blue cone, and between ON and OFF bipolar cell populations are demonstrated on independent bedding. Specificity shows which cell type indicated the gene more highly. For pan BC vs pole and cone, genes identified as putative transcription factors are recognized by their TF family. Genes absent from your Drop-seq data demonstrated in Number 2source data 1 are indicated among those that are differentially indicated between ON and OFF bipolar cells. elife-48216-supp5.xlsx (729K) DOI:?10.7554/eLife.48216.023 Supplementary file 6: GO analysis of differentially expressed genes. Enriched GO terms for biological processes from Outputs for genes enriched in photoreceptor and bipolar cells are demonstrated on separate bedding. Input gene lists were filtered based on fold-change NHS-Biotin in manifestation and minimum go through counts to identify those most NHS-Biotin highly enriched in photoreceptor (n?=?818) and bipolar cells (n?=?832). A list of all genes recognized by RNA-seq in either cell class was used like a research. elife-48216-supp6.xlsx (52K) DOI:?10.7554/eLife.48216.024 Supplementary file 7: Differentially accessible areas. ATAC-seq peaks, normalized read counts, fold-change values, modified p-values and assigned genes are outlined on separate bedding for each assessment. Specificity shows the cell type in which the maximum is more highly accessible. Shared-unfiltered peaks are those that are not differentially accessible when comparing bipolar cells versus photoreceptors (fold-change ideals? ?2 and -2). Retina peaks are those demonstrated in Number 5A; they have been filtered to remove those accessible in B cells, brain and liver. Peaks with correlated gene manifestation identified in Number 5C and Number 5figure product 1D are indicated. elife-48216-supp7.xlsx (23M) DOI:?10.7554/eLife.48216.025 Supplementary file 8: Known motifs enriched in enhancers of bipolar cell populations. Enrichment of all 319 motifs in the HOMER database for those, ON-, and OFF-bipolar cells, each on independent sheets. A assessment of the proportional enrichment for each motif between aggregate bipolar cells and pole, blue and green cones is included on a separate sheet. A complete list of sequence logos and position excess weight matrices for individual motifs is available on-line in the HOMER motif database: elife-48216-supp8.xlsx (165K) DOI:?10.7554/eLife.48216.026 Transparent reporting form. elife-48216-transrepform.docx (247K) DOI:?10.7554/eLife.48216.027 Data Availability StatementSequencing data have been deposited in GEO under accession code “type”:”entrez-geo”,”attrs”:”text”:”GSE131625″,”term_id”:”131625″GSE131625. The following dataset was generated: Murphy DP, Hughes AE, Rabbit Polyclonal to APLP2 Lawrence KA, Myers CA, Corbo JC. 2019. Cis-regulatory basis of sister cell type divergence in the vertebrate retina. NCBI Gene Manifestation Omnibus. GSE131625 The following previously published datasets were used: Hughes AE, Enright JM, Myers CA, Shen SQ, Corbo JC. 2017. ATAC-seq and RNA-seq of adult mouse rods and cones. NCBI Gene Manifestation Omnibus. GSE83312 John Stamatoyannopoulos. 2012. DNase on 8 week adult mouse retina. ENCODE. ENCSR000CNW John Stamatoyannopoulos. 2011. DNase-seq.