Additional file 1: of Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes

This file contains a mini-website of Tables S1-S10. The same mini-website is available at http://carterdev.jax.org/dtx/a2/index.html. Interactive expression plots. Table S1. Number and proportion of isolated cells for cytological analysis and RNA-seq. Table S2. Gene lists and gene expression values for each of the substages, separated by worksheets. An additional worksheet provides results for X-linked genes. Abbreviations for each substage are as follows: Sp’gonia for spermatogonia, PL for preleptotene, EL for early leptotene, LL + Z for late leptotene and zygotene, LL + Z + EP for those genes found in late leptotene, zygotene, and early pachytene, EP for early pachytene, EP + LP + D for early pachytene, late pachytene, and diplotene, and LP + D for late pachytene and diplotene. Sheet names prefixed with “Anti-“correspond to genes that are negatively concordant with the substage, (e.g., Anti-PL corresponds to genes that are negatively concordant with preleptotene. Genes are ranked by how closely the expression pattern follows the substage pattern (rank = 1 is best). Gene ids and Gene names for piRNA precursors and NONCODE lncRNAs have prefix “pi-” and “NON”, respectively. Expression is given in log2(TPM + 1). Table S3. GO analysis for substage-negatively concordant genes. Abbreviations for each substage are as follows: Sp’gonia for spermatogonia, EL for early leptotene, LL-Z for late leptotene and zygotene, EP for early pachytene, and LP-D for late pachytene and diplotene. Table S4. GO analysis for substage-concordant genes. Abbreviations for each substage are as follows: Sp’gonia for spermatogonia, EL for early leptotene, LL-Z for late leptotene and zygotene, EP for early pachytene, and LP-D for late pachytene and diplotene. Table S5. Analysis of genes annotated to meiosis. Table S6. TFs for substage-concordant genes. The column names are explained as follows: “NES” is short for Normalized Enrichment Score in iRegulon, “ngenes” is the number of substage-concordant genes associated with the TF, “name” used in the arc-diagram (* indicates a family of genes, e.g., Rfx* for Rfx1, Rfx2, Rfx3, Rfx4). Bolded TFs are highly expressed in the testis and those highlighted in red are associated with male reproduction. Table S7. TFs for substage-negatively concordant genes. The column names are explained as follows: “NES” is short for Normalized Enrichment Score in iRegulon, “ngenes” is the number of substage negatively-concordant genes associated with the TF, “name” used in the arc-diagram (* indicates a family of genes, e.g., Rfx* for Rfx1, Rfx2, Rfx3, Rfx4). Table S8. Comparison of substage-concordant gene lists with derived clusters in Margolin, et al. [14]. Table S9. Comparison of substage-concordant gene lists with sets derived from FACS-sorted cells [5, 6]. Table S10. Primers for qRT-PCR. (ZIP 6513 kb)