{"id":4221,"date":"2019-06-30T06:36:08","date_gmt":"2019-06-30T06:36:08","guid":{"rendered":"http:\/\/biodigestor.net\/?p=4221"},"modified":"2019-06-30T06:36:08","modified_gmt":"2019-06-30T06:36:08","slug":"supplementary-materialsdocument-s1-in-at-least-one-input-sample-are-highlighted","status":"publish","type":"post","link":"https:\/\/biodigestor.net\/?p=4221","title":{"rendered":"Supplementary MaterialsDocument S1. in at least one input sample) are highlighted"},"content":{"rendered":"

Supplementary MaterialsDocument S1. in at least one input sample) are highlighted in gray and were excluded from downstream analyses. This file contains six worksheets (xlsx format). mmc2.xlsx (3.5M) GUID:?0AAB377E-AC3C-4D46-B7B9-E03E690448AE Table S2. List of All HP1-Enriched Genes that Have Orthologs in at Least One Other Species, Related to Figures 1 and 2 and Tables 733767-34-5 S1 and S7 Columns A and B: gene IDs and annotations. Column C: HP1 enrichment values (ChIP\/input ratio). Column D: heterochromatic gene family classification. Columns E and F: species encoding an ortholog or syntenic ortholog. Column 733767-34-5<\/a> G: number of species in which the orthologous gene is HP1-enriched. Columns H and AB: gene IDs of orthologs in Clones A1-H.1 and A1-C.1, Related to Figure?3 and Tables S1 and S7 ChIP\/input enrichment values were calculated over a 1,000-bp window (ATG?500?bp) for each coding sequence of the reference genome in clones A1-H.1 and A1-C.1 schizont stages. Column A: chromosome number. Columns B and C: nucleotide positions at the start and end of each 1,000-bp window. Columns D and E: gene IDs and annotations. Columns FCI: RPKM values for the -ChIP and input samples for each of the two clones. Columns J and K: PkHP1 enrichment values (ChIP\/input ratio) for each of the two clones. Column L: fold change in PkHP1 occupancy in A1-H.1 compared with A1-C.1. Genes with 2.5-fold higher or lower PkHP1 occupancy in A1-H.1 are highlighted in light or dark orange, respectively. The ChIP-seq values for clone A1-C.1 are identical to those listed in Table S1. Genes with very low mappability (RPKM value 5 in at least one input sample) are highlighted in gray and were excluded from downstream analyses (xlsx format). mmc4.xlsx (767K) GUID:?95B6E901-FD1D-4EF6-AECA-288B21604B0A Table S4. Genome-wide HP1 Occupancy in Four Different Strains, Linked to Numbers 4 and Dining tables and S4 S1 and S7 ChIP\/insight enrichment ideals had been determined more than a IL1-ALPHA<\/a> 1,000-bp windowpane (ATG?500?bp) for every coding sequence of the 3D7 reference genome in schizont stages of strains Pf2004, NF135, NF54, and 3D7. Column A: chromosome number. Columns B and C: nucleotide positions at the start and end of each 1,000-bp window. Columns D and E: gene IDs and annotations. Columns FCM: RPKM values for the -ChIP and input samples for each of the four strains. Columns NCQ: PfHP1 enrichment values (ChIP\/input ratio) for each of the four strains. Columns RCU: (Rovira-Graells et?al., 2012). Column Z: degree of variation in gene expression (SD) in field samples (Mok et?al., 2015). Genes with variable PfHP1 occupancy between the strains are marked in blue (k-means clusters 5C11). Genes with very low mappability (RPKM value 5 in at least one input sample) are highlighted in gray and were excluded from downstream analyses. The ChIP-seq values for 3D7 schizonts are identical to those listed in Tables S1 and S5 (xlsx format). mmc5.xlsx (1.4M) GUID:?7F5DEE94-8F10-474E-AAAA-CFAD5C47A1CA Table S5. Genome-wide PfHP1 Occupancy in Ring Stages, Trophozoites, and Schizonts, 733767-34-5 Related to Figure?5 and Tables S1 and S7 ChIP\/input enrichment values were calculated over a 1000-bp window (ATG? 500?bp) for each coding sequence of the 3D7 reference genome in ring stages, trophozoite, and schizont stages of 3D7 parasites. Column A: chromosome number. Columns B and C: nucleotide positions at the start and end of each 1,000-bp window. Columns D and E: gene IDs and annotations. Columns FCH: RPKM values for the -ChIP samples for each of the three IDC stages. Column I: RPKM values for the input sample from schizonts. Columns JCL: PfHP1 enrichment values (ChIP\/input ratio) for each of the three IDC stages. Column M: peak transcript abundance during the IDC.<\/p>\n","protected":false},"excerpt":{"rendered":"

Supplementary MaterialsDocument S1. in at least one input sample) are highlighted in gray and were excluded from downstream analyses. This file contains six worksheets (xlsx format). mmc2.xlsx (3.5M) GUID:?0AAB377E-AC3C-4D46-B7B9-E03E690448AE Table S2. List of All HP1-Enriched Genes that Have Orthologs in at Least One Other Species, Related to Figures 1 and 2 and Tables 733767-34-5 S1… Continue reading Supplementary MaterialsDocument S1. in at least one input sample) are highlighted<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[111],"tags":[3746,3723],"class_list":["post-4221","post","type-post","status-publish","format-standard","hentry","category-5-ht-uptake","tag-733767-34-5","tag-il1-alpha","entry"],"_links":{"self":[{"href":"https:\/\/biodigestor.net\/index.php?rest_route=\/wp\/v2\/posts\/4221"}],"collection":[{"href":"https:\/\/biodigestor.net\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/biodigestor.net\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/biodigestor.net\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/biodigestor.net\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=4221"}],"version-history":[{"count":1,"href":"https:\/\/biodigestor.net\/index.php?rest_route=\/wp\/v2\/posts\/4221\/revisions"}],"predecessor-version":[{"id":4222,"href":"https:\/\/biodigestor.net\/index.php?rest_route=\/wp\/v2\/posts\/4221\/revisions\/4222"}],"wp:attachment":[{"href":"https:\/\/biodigestor.net\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4221"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/biodigestor.net\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4221"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/biodigestor.net\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4221"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}