DOI: 10.6084/m9.figshare.7496147.v1
title: Loss of Nmp4 optimizes osteogenic metabolism and secretion to enhance bone quality

description: Supplemental tables.<b>Supplemental Table S1:</b> ChIP-seq data, located in separate xlsx file GEO accession number GSE112693 for complete ChIP-Seq datasetNmp4 occupancy sties in MC3T3-E1 osteoblast-like cells as determined by ChIP-seq analysis (Childress et al., 2015). Peaks are mapped to mouse genome build mm10. Column A: gene IDs from Ensembl genes, UCSC genes, etc; Column B: gene symbol; Column C: strand; Column D: chromosome; Column E: location of transcription start site (TSS); Column F: location of transcription end site (TES); Column G: Location of Nmp4 in Zones 1-4. A peak was assigned to a promoter region if it was within -5 to+2 kb from a transcription start site (TSS, Zone 1). The Nmp4 peak was assigned to Zone 2, the intragenic region, if it was located within the range defined by the TSS and the transcription end site, and not within the promoter range of the same gene. To assign a peak to Zone 3, the intergenic region, it had to be -10 000 kb from the TSS and +10 000 kb from the transcription end site, and not within the promoter range of the same gene. Peaks that did not fit any of these definitions were assigned to the classification “other” (Zone 4). A peak could be assigned to multiple functional regions in an area of the genome harboring multiple genes. Note for Nmp4 gene occupancy we used genes identified in Zones 1 & 2 and listed in Supplemental Table 2. Column H: Peak_start, the recorded peak start position; Column I: Peak_end: the recorded peak end position; Column J: Peak_position, the middle point position of a peak; Column K: Peak_value, the peak score. This parameter is the measurement of overall (usually average) enrichment for the region.<b>Supplemental Table S2: </b>RNA-seq data, located in separate xlsx file [GEO accession number GSE112694] Expression of all genes was normalized based on the expression of Gusb (see Materials and Methods). The columns are defined as follows (also see file)<br><b>Supplemental Table S3:</b> Day 3 IPA canonical pathways, located in separate xls fileIPA Canonical pathways perturbed by loss of Nmp4 in MPSCs harvested at Day 3 in culture. Pathways were identified as significantly sensitive to Nmp4 status that achieved a value of –log(p-value) ≥1.30. • Column A: identity of the canonical pathway; • Column B: –log(p-value); • Column C: Ratio, the number of genes listed in the dataset over the total number of genes in the pathway. • Column D z-score of pathway. The activation state of the pathway is predicted to be increased if the z-score is ≥ 2 and attenuated if the z-score ≤ −2. Those pathways listed as #NUM indicate that the z-score algorithm cannot predict whether the pathway activity is increased or decreased in the Nmp4-/- cells. • Column E: molecules in the dataset belonging to pathway.<b>Supplemental Table S4:</b> Day 7 IPA canonical pathways, located in separate xls fileIPA Canonical pathways perturbed by loss of Nmp4 in MPSCs harvested at Day 7 in culture. Pathways were identified as significantly sensitive to Nmp4 status that achieved a value of –log(p-value) ≥1.30. See Supplemental Table S3 legend for identity of table columns. <br><br><br>