Expression Values
Count Matrices
Summary of Available Data
| Feature Counts | |||||
| Species | Gene | Epimachine | miRNA | lncRNA | mCpG |
|---|---|---|---|---|---|
| Acropora pulchra | 44,371 | 326 | 51 | 15,559 | 6,566,306 |
| Porites evermanni | 40,389 | 324 | 48 | 8,319 | 4,751,249 |
| Pocillopora tuahiniensis | 31,840 | 326 | 40 | 11,236 | 6,020,191 |
ConTra
If you are excited about analyzing this type of data in contextual manner check out ConTra - Contextual Transcriptome Regulation Analysis
About Computational Pipelines
This workflow aligns trimmed RNA-seq reads to a reference genome using HISAT2, followed by transcript assembly and quantification with StringTie, and culminates in the generation of count matrices for downstream expression analysis. Individual sample directories contain BAMs, indexes, GTFs, Ballgown-formatted tables, and alignment statistics, while a MultiQC report aggregates overall alignment quality. The workflow then merges sorted BAMs into a single dataset, compiles a unified transcript GTF from individual assemblies, and uses prepDE to produce gene- and transcript-level count matrices compatible with DESeq2.
Workflow processes sRNA-seq reads through quality control and adapter trimming with fastp, then performs miRNA discovery and quantification using ShortStack 4.1.0. ShortStack aligns trimmed reads to the species-specific genome reference and integrates a curated cnidarian miRBase database for known miRNA annotation. De novo miRNA identification is performed using the --dn_mirna parameter, which predicts novel miRNA loci based on hairpin structure and expression patterns. The pipeline generates comprehensive count matrices across all samples, with only confirmed miRNA loci (MIRNA=“Y” in Results.txt) retained for downstream analysis.
Workflow builds a splice-aware HISAT2 index from the GTF (exons + splice sites), and aligns all samples. Per-sample transcript assemblies are generated with StringTie and merged into a unified GTF, which is then annotated with gffcompare. Putative lncRNAs are filtered from the merged annotations by biotype/class codes (u/x/o/i) and minimum length (>200 nt), sequences are extracted with bedtools, and coding potential is screened with CPC2 to retain noncoding transcripts. The surviving transcripts are converted into a clean BED/GTF set with unique lncRNA_### IDs, deduplicated, sanity-checked (coordinates/lengths), and summarized. Finally, featureCounts quantifies lncRNA features across all BAMs, column names are cleaned, and a filtered count matrix is produced, removing features with <10 counts in >50% of samples.
For EM-seq analysis Bismark methylation coverage (.cov) files are unified into CpG methylation matrices. First, .cov.gz are filtered for CpG sites with ≥10× coverage and converts them into bedgraph files. Each bedgraph is reformatted into a simplified two-column _processed.txt file containing unique CpG IDs and percent methylation values. A Python script then merges all _processed.txt files into a single matrix, with CpG loci as rows and samples as columns. Only loci where 10x coverage is present in all samples are retained.
Sample Counts by Data Type
| Sample Counts by Data Type | |||||
| Species | Gene | Epimachine | miRNA | lncRNA | mCpG |
|---|---|---|---|---|---|
| Acropora pulchra | 40 | 40 | 40 | 40 | 39 |
| Porites evermanni | 38 | 38 | 37 | 38 | 37 |
| Pocillopora tuahiniensis | 39 | 39 | 39 | 39 | 32 |
Acropora pulchra
Gene
https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-RNAseq-alignment-HiSat2/apul-gene_count_matrix.csv Apul_gene (first 4 rows)
| gene_id | ACR-139-TP1 | ACR-139-TP2 | ACR-139-TP3 | ACR-139-TP4 | ACR-145-TP1 | ACR-145-TP2 | ACR-145-TP3 | ACR-145-TP4 | ACR-150-TP1 | ACR-150-TP2 | ACR-150-TP3 | ACR-150-TP4 | ACR-173-TP1 | ACR-173-TP2 | ACR-173-TP3 | ACR-173-TP4 | ACR-186-TP1 | ACR-186-TP2 | ACR-186-TP3 | ACR-186-TP4 | ACR-225-TP1 | ACR-225-TP2 | ACR-225-TP3 | ACR-225-TP4 | ACR-229-TP1 | ACR-229-TP2 | ACR-229-TP3 | ACR-229-TP4 | ACR-237-TP1 | ACR-237-TP2 | ACR-237-TP3 | ACR-237-TP4 | ACR-244-TP1 | ACR-244-TP2 | ACR-244-TP3 | ACR-244-TP4 | ACR-265-TP1 | ACR-265-TP2 | ACR-265-TP3 | ACR-265-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FUN_002326 | 3 | 2 | 3 | 4 | 12 | 7 | 7 | 16 | 21 | 3 | 10 | 11 | 19 | 6 | 24 | 17 | 1 | 2 | 2 | 3 | 20 | 15 | 13 | 11 | 2 | 1 | 1 | 0 | 16 | 16 | 14 | 24 | 2 | 1 | 3 | 1 | 18 | 9 | 5 | 12 |
| FUN_002315 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| FUN_002316 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| FUN_002303 | 10 | 5 | 10 | 10 | 23 | 18 | 20 | 38 | 38 | 6 | 40 | 30 | 73 | 18 | 73 | 31 | 3 | 5 | 4 | 9 | 34 | 54 | 38 | 21 | 2 | 2 | 3 | 1 | 45 | 37 | 36 | 51 | 3 | 4 | 12 | 3 | 31 | 29 | 23 | 23 |
Epigenetic Machinery
https://raw.githubusercontent.com/urol-e5/timeseries_molecular/refs/heads/main/D-Apul/output/36-Apul-epimachine-counts/Apul-epimachine-expression.csv Apul_epimachine (first 4 rows)
| gene_id | protein_match | ACR-139-TP1 | ACR-139-TP2 | ACR-139-TP3 | ACR-139-TP4 | ACR-145-TP1 | ACR-145-TP2 | ACR-145-TP3 | ACR-145-TP4 | ACR-150-TP1 | ACR-150-TP2 | ACR-150-TP3 | ACR-150-TP4 | ACR-173-TP1 | ACR-173-TP2 | ACR-173-TP3 | ACR-173-TP4 | ACR-186-TP1 | ACR-186-TP2 | ACR-186-TP3 | ACR-186-TP4 | ACR-225-TP1 | ACR-225-TP2 | ACR-225-TP3 | ACR-225-TP4 | ACR-229-TP1 | ACR-229-TP2 | ACR-229-TP3 | ACR-229-TP4 | ACR-237-TP1 | ACR-237-TP2 | ACR-237-TP3 | ACR-237-TP4 | ACR-244-TP1 | ACR-244-TP2 | ACR-244-TP3 | ACR-244-TP4 | ACR-265-TP1 | ACR-265-TP2 | ACR-265-TP3 | ACR-265-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FUN_000231 | Kmt7-Setd7/9-201 | 1591 | 2000 | 949 | 1842 | 1094 | 890 | 573 | 1172 | 916 | 923 | 1881 | 1459 | 708 | 1434 | 1181 | 682 | 625 | 1070 | 552 | 1394 | 889 | 2004 | 2041 | 679 | 1701 | 1565 | 1515 | 1137 | 784 | 1039 | 1854 | 1106 | 783 | 1764 | 2197 | 599 | 888 | 1449 | 1348 | 1359 |
| FUN_000374 | PRDM7-202 | 63 | 121 | 112 | 29 | 60 | 32 | 40 | 36 | 44 | 67 | 162 | 61 | 31 | 75 | 86 | 21 | 50 | 206 | 72 | 77 | 51 | 157 | 114 | 35 | 243 | 132 | 215 | 0 | 36 | 101 | 164 | 64 | 22 | 185 | 185 | 31 | 29 | 117 | 55 | 23 |
| FUN_000535 | Mbd4-201 | 106 | 187 | 136 | 162 | 118 | 99 | 118 | 196 | 116 | 168 | 366 | 193 | 57 | 56 | 275 | 86 | 0 | 161 | 147 | 110 | 168 | 192 | 276 | 49 | 157 | 384 | 259 | 66 | 125 | 247 | 266 | 118 | 115 | 342 | 228 | 103 | 120 | 557 | 186 | 160 |
| FUN_001019 | USP47-207 | 1553 | 2067 | 1290 | 1498 | 1044 | 1035 | 866 | 996 | 827 | 1144 | 1985 | 2263 | 773 | 1019 | 990 | 567 | 396 | 1675 | 1035 | 1613 | 1023 | 1561 | 1684 | 760 | 2156 | 1693 | 1803 | 897 | 1461 | 1130 | 1713 | 1346 | 780 | 1314 | 1684 | 1005 | 1248 | 1551 | 1401 | 1345 |
miRNA
https://raw.githubusercontent.com/urol-e5/timeseries_molecular/refs/heads/main/M-multi-species/output/10-format-miRNA-counts/Apul_miRNA_counts_formatted.txt Apul_mirna (first 4 rows)
| Name | 1A10_ACR-145_TP4 | 1A12_ACR-237_TP3 | 1A1_ACR-173_TP1 | 1A2_ACR-244_TP4 | 1A8_ACR-186_TP2 | 1A9_ACR-244_TP2 | 1B10_ACR-150_TP4 | 1B1_ACR-225_TP3 | 1B2_ACR-173_TP3 | 1B5_ACR-229_TP1 | 1B9_ACR-265_TP4 | 1C10_ACR-173_TP4 | 1C4_ACR-139_TP4 | 1D10_ACR-265_TP2 | 1D3_ACR-225_TP4 | 1D4_ACR-237_TP4 | 1D6_ACR-229_TP2 | 1D8_ACR-237_TP2 | 1D9_ACR-229_TP4 | 1E1_ACR-265_TP3 | 1E3_ACR-150_TP2 | 1E5_ACR-139_TP3 | 1E9_ACR-237_TP1 | 1F11_ACR-173_TP2 | 1F4_ACR-150_TP3 | 1F8_ACR-145_TP3 | 1G5_ACR-244_TP3 | 1H11_ACR-225_TP1 | 1H12_ACR-186_TP3 | 1H6_ACR-225_TP2 | 1H7_ACR-229_TP3 | 1H8_ACR-186_TP4 | 2B2_ACR-145_TP1 | 2B3_ACR-139_TP2 | 2C1_ACR-244_TP1 | 2C2_ACR-139_TP1 | 2D2_ACR-150_TP1 | 2E2_ACR-186_TP1 | 2F1_ACR-265_TP1 | 2G1_ACR-145_TP2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cluster_1819 | 37 | 35 | 102 | 77 | 84 | 340 | 14 | 19 | 36 | 204 | 25 | 18 | 10 | 96 | 66 | 41 | 195 | 81 | 66 | 19 | 177 | 2 | 19 | 88 | 56 | 23 | 95 | 18 | 33 | 47 | 50 | 28 | 44 | 68 | 57 | 50 | 22 | 24 | 16 | 62 |
| Cluster_1832 | 325 | 435 | 1826 | 947 | 1238 | 2174 | 219 | 580 | 547 | 3544 | 223 | 235 | 211 | 618 | 2897 | 978 | 2836 | 645 | 1098 | 265 | 1326 | 45 | 288 | 1527 | 757 | 214 | 2749 | 610 | 439 | 1714 | 805 | 873 | 232 | 1769 | 788 | 1115 | 144 | 211 | 171 | 1032 |
| Cluster_1833 | 16 | 52 | 40 | 30 | 6 | 0 | 6 | 27 | 30 | 145 | 6 | 3 | 13 | 0 | 82 | 94 | 30 | 57 | 12 | 21 | 0 | 0 | 19 | 24 | 12 | 7 | 0 | 20 | 11 | 38 | 11 | 42 | 0 | 18 | 53 | 24 | 4 | 0 | 0 | 27 |
| Cluster_1836 | 1071 | 2048 | 2334 | 6240 | 8001 | 11364 | 1614 | 2024 | 1577 | 5523 | 1993 | 885 | 1073 | 2737 | 14727 | 10196 | 8094 | 4832 | 4571 | 1210 | 5111 | 747 | 1425 | 4717 | 3174 | 1026 | 4302 | 1059 | 1636 | 6727 | 2155 | 1625 | 1266 | 5844 | 2033 | 2926 | 1267 | 1729 | 656 | 8817 |
lncRNA
https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/D-Apul/output/31.5-Apul-lncRNA-discovery/lncRNA_counts.clean.filtered.txt Apul_lncRNA (first 4 rows)
| Geneid | Chr | Start | End | Strand | Length | ACR-139-TP1 | ACR-139-TP2 | ACR-139-TP3 | ACR-139-TP4 | ACR-145-TP1 | ACR-145-TP2 | ACR-145-TP3 | ACR-145-TP4 | ACR-150-TP1 | ACR-150-TP2 | ACR-150-TP3 | ACR-150-TP4 | ACR-173-TP1 | ACR-173-TP2 | ACR-173-TP3 | ACR-173-TP4 | ACR-186-TP1 | ACR-186-TP2 | ACR-186-TP3 | ACR-186-TP4 | ACR-225-TP1 | ACR-225-TP2 | ACR-225-TP3 | ACR-225-TP4 | ACR-229-TP1 | ACR-229-TP2 | ACR-229-TP3 | ACR-229-TP4 | ACR-237-TP1 | ACR-237-TP2 | ACR-237-TP3 | ACR-237-TP4 | ACR-244-TP1 | ACR-244-TP2 | ACR-244-TP3 | ACR-244-TP4 | ACR-265-TP1 | ACR-265-TP2 | ACR-265-TP3 | ACR-265-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| lncRNA_015 | ntLink_2 | 327086 | 329262 | + | 2177 | 113.00 | 2.00 | 2.0 | 114.00 | 154.00 | 20.00 | 90.00 | 106 | 268.0 | 37.00 | 108.00 | 26.00 | 430.00 | 36.00 | 16 | 99.0 | 32 | 7.00 | 29.0 | 37.0 | 15.00 | 267.0 | 43.00 | 8.0 | 4.00 | 45.0 | 107.00 | 66 | 22.00 | 58.0 | 29.00 | 104.0 | 6.0 | 32.0 | 181 | 38.00 | 5.0 | 76.00 | 254 | 43.00 |
| lncRNA_076 | ntLink_6 | 48577 | 50741 | + | 2165 | 48.00 | 19.00 | 23.0 | 10.00 | 50.00 | 11.00 | 49.00 | 72 | 33.0 | 44.00 | 19.00 | 0.00 | 13.00 | 38.00 | 24 | 6.0 | 54 | 122.00 | 40.0 | 69.0 | 66.00 | 47.0 | 26.00 | 5.0 | 59.00 | 68.0 | 96.00 | 178 | 42.00 | 60.0 | 23.00 | 4.0 | 116.0 | 109.0 | 58 | 67.00 | 147.0 | 106.00 | 109 | 28.00 |
| lncRNA_077 | ntLink_6 | 191068 | 194203 | + | 3136 | 648.25 | 694.75 | 958.5 | 764.75 | 846.25 | 488.75 | 1035.25 | 585 | 719.5 | 590.75 | 671.25 | 839.75 | 622.75 | 417.75 | 1084 | 848.5 | 625 | 932.08 | 1325.5 | 888.5 | 870.75 | 711.5 | 947.75 | 782.5 | 929.25 | 914.5 | 837.25 | 786 | 1060.75 | 680.2 | 672.75 | 1327.5 | 697.5 | 834.5 | 823 | 1132.75 | 1188.5 | 812.25 | 735 | 982.25 |
| lncRNA_078 | ntLink_6 | 191227 | 194203 | + | 2977 | 648.25 | 694.75 | 958.5 | 764.75 | 846.25 | 488.75 | 1035.25 | 585 | 719.5 | 590.75 | 671.25 | 839.75 | 622.75 | 417.75 | 1084 | 848.5 | 625 | 931.08 | 1325.5 | 888.5 | 870.75 | 711.5 | 947.75 | 782.5 | 929.25 | 914.5 | 837.25 | 786 | 1060.75 | 680.2 | 672.75 | 1327.5 | 697.5 | 834.5 | 823 | 1132.75 | 1188.5 | 812.25 | 735 | 982.25 |
mCpG Percentage
https://gannet.fish.washington.edu/metacarcinus/E5/20250903_meth_Apul/merged-WGBS-CpG-counts_filtered_n20.csv Apul_mCpG (first 4 rows)
| CpG | ACR-145-TP3 | ACR-265-TP4 | ACR-139-TP3 | ACR-244-TP1 | ACR-237-TP1 | ACR-265-TP3 | ACR-186-TP4 | ACR-186-TP2 | ACR-244-TP4 | ACR-225-TP3 | ACR-139-TP2 | ACR-186-TP1 | ACR-145-TP1 | ACR-145-TP4 | ACR-225-TP4 | ACR-173-TP3 | ACR-150-TP4 | ACR-173-TP1 | ACR-173-TP2 | ACR-237-TP3 | ACR-265-TP1 | ACR-186-TP3 | ACR-229-TP1 | ACR-229-TP2 | ACR-150-TP3 | ACR-173-TP4 | ACR-225-TP2 | ACR-244-TP2 | ACR-150-TP2 | ACR-237-TP2 | ACR-265-TP2 | ACR-229-TP4 | ACR-244-TP3 | ACR-150-TP1 | ACR-139-TP1 | ACR-145-TP2 | ACR-139-TP4 | ACR-229-TP3 | ACR-237-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CpG_ntLink_0_90500 | 0 | 0 | 0 | NA | NA | 0 | 0.000000 | 1.851852 | NA | NA | 0 | 0 | 0 | 0.000000 | 0 | NA | NA | NA | NA | NA | 0 | 0 | 0.000000 | 0 | NA | NA | 0.000000 | NA | NA | NA | 4.166667 | 0 | NA | NA | 0.000000 | 0.000000 | 0 | 0 | NA |
| CpG_ntLink_0_90540 | 0 | 0 | 0 | NA | NA | 0 | 0.000000 | 2.985075 | NA | NA | 0 | 0 | 0 | 3.448276 | 0 | NA | NA | 0 | NA | NA | 0 | 0 | 0.000000 | 0 | NA | NA | 0.000000 | NA | NA | 0 | 0.000000 | 0 | NA | 0 | 0.000000 | 2.631579 | 0 | 0 | NA |
| CpG_ntLink_0_90562 | 0 | 0 | 0 | NA | NA | 0 | 0.000000 | 1.428571 | NA | NA | 0 | 0 | 0 | 0.000000 | 0 | NA | 0 | 0 | 0 | NA | 0 | 0 | 0.000000 | 0 | NA | NA | 0.000000 | NA | NA | 0 | 0.000000 | 0 | NA | 0 | 0.000000 | 2.439024 | 0 | 0 | NA |
| CpG_ntLink_0_90633 | 0 | NA | 0 | NA | NA | 0 | 2.857143 | 3.030303 | NA | NA | 0 | 0 | 0 | 0.000000 | 0 | NA | NA | NA | NA | NA | 0 | 0 | 4.545455 | 0 | NA | NA | 8.333333 | NA | NA | NA | 0.000000 | 0 | NA | NA | 5.882353 | 0.000000 | 0 | 0 | NA |
Porites evermanni
Gene
https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/02.20-E-Peve-RNAseq-alignment-HiSat2/peve-gene_count_matrix.csv Peve_gene (first 4 rows)
| gene_id | POR-216-TP1 | POR-216-TP2 | POR-216-TP3 | POR-216-TP4 | POR-236-TP1 | POR-236-TP2 | POR-245-TP1 | POR-245-TP2 | POR-245-TP3 | POR-245-TP4 | POR-260-TP1 | POR-260-TP2 | POR-260-TP3 | POR-260-TP4 | POR-262-TP1 | POR-262-TP2 | POR-262-TP3 | POR-262-TP4 | POR-69-TP1 | POR-69-TP2 | POR-69-TP3 | POR-69-TP4 | POR-72-TP1 | POR-72-TP2 | POR-72-TP3 | POR-72-TP4 | POR-73-TP1 | POR-73-TP2 | POR-73-TP3 | POR-73-TP4 | POR-74-TP1 | POR-74-TP2 | POR-74-TP3 | POR-74-TP4 | POR-83-TP1 | POR-83-TP2 | POR-83-TP3 | POR-83-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| gene-Peve_00000032 | 29 | 75 | 63 | 25 | 82 | 39 | 25 | 23 | 7 | 44 | 42 | 20 | 13 | 28 | 35 | 78 | 108 | 67 | 43 | 25 | 30 | 19 | 38 | 30 | 34 | 65 | 21 | 9 | 23 | 27 | 14 | 28 | 15 | 9 | 63 | 11 | 33 | 27 |
| gene-Peve_00000122 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 1 | 1 | 1 |
| gene-Peve_00000008 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 19 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| gene-Peve_00000117 | 13 | 13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 |
Epigenetic Machinery
https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/E-Peve/output/14-Peve-epimachine-exp/Peve-epimachine-expression.csv Peve_epimachine (first 4 rows)
| gene_id | protein_match | POR-216-TP1 | POR-216-TP2 | POR-216-TP3 | POR-216-TP4 | POR-236-TP1 | POR-236-TP2 | POR-245-TP1 | POR-245-TP2 | POR-245-TP3 | POR-245-TP4 | POR-260-TP1 | POR-260-TP2 | POR-260-TP3 | POR-260-TP4 | POR-262-TP1 | POR-262-TP2 | POR-262-TP3 | POR-262-TP4 | POR-69-TP1 | POR-69-TP2 | POR-69-TP3 | POR-69-TP4 | POR-72-TP1 | POR-72-TP2 | POR-72-TP3 | POR-72-TP4 | POR-73-TP1 | POR-73-TP2 | POR-73-TP3 | POR-73-TP4 | POR-74-TP1 | POR-74-TP2 | POR-74-TP3 | POR-74-TP4 | POR-83-TP1 | POR-83-TP2 | POR-83-TP3 | POR-83-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| gene-Peve_00000002 | USP1-201 | 8 | 16 | 16 | 8 | 0 | 8 | 13 | 9 | 0 | 17 | 37 | 2 | 5 | 0 | 0 | 7 | 13 | 16 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 7 | 4 | 0 | 9 | 0 | 5 | 8 |
| gene-Peve_00000025 | NAA60-202 | 93 | 63 | 41 | 31 | 178 | 60 | 92 | 33 | 31 | 50 | 114 | 50 | 37 | 30 | 74 | 73 | 92 | 45 | 119 | 41 | 78 | 51 | 48 | 74 | 106 | 79 | 67 | 43 | 13 | 34 | 57 | 6 | 74 | 4 | 60 | 34 | 34 | 54 |
| gene-Peve_00000085 | DUS1L-201 | 70 | 81 | 19 | 32 | 55 | 24 | 114 | 34 | 25 | 67 | 158 | 35 | 25 | 43 | 48 | 77 | 58 | 37 | 17 | 73 | 28 | 17 | 76 | 48 | 76 | 61 | 36 | 48 | 17 | 19 | 60 | 30 | 32 | 20 | 35 | 49 | 12 | 18 |
| gene-Peve_00000091 | ALYREF-202 | 1212 | 1264 | 319 | 210 | 1005 | 356 | 917 | 400 | 288 | 337 | 1169 | 371 | 315 | 351 | 844 | 523 | 717 | 601 | 453 | 548 | 372 | 311 | 578 | 686 | 651 | 969 | 367 | 306 | 183 | 408 | 702 | 205 | 355 | 273 | 391 | 420 | 248 | 239 |
miRNA
https://raw.githubusercontent.com/urol-e5/timeseries_molecular/refs/heads/main/M-multi-species/output/10-format-miRNA-counts/Peve_miRNA_counts_formatted.txt Peve_mirna (first 4 rows)
| Name | 1A11_POR-216_TP2 | 1A7_POR-73_TP1 | 1B3_POR-83_TP3 | 1B4_POR-72_TP1 | 1B6_POR-260_TP4 | 1B7_POR-245_TP2 | 1C11_POR-74_TP4 | 1C12_POR-72_TP3 | 1C5_POR-73_TP3 | 1C6_POR-262_TP2 | 1D12_POR-260_TP2 | 1D1_POR-245_TP4 | 1D2_POR-245_TP1 | 1D5_POR-260_TP1 | 1D7_POR-74_TP1 | 1E7_POR-69_TP4 | 1F10_POR-260_TP3 | 1F12_POR-72_TP4 | 1F1_POR-73_TP2 | 1F3_POR-83_TP2 | 1F6_POR-69_TP1 | 1F7_POR-83_TP4 | 1G10_POR-74_TP2 | 1G1_POR-262_TP1 | 1G3_POR-74_TP3 | 1H1_POR-245_TP3 | 1H2_POR-73_TP4 | 1H3_POR-83_TP1 | 2A3_POR-262_TP4 | 2B1_POR-72_TP2 | 2D1_POR-236_TP1 | 2D3_POR-262_TP3 | 2E1_POR-216_TP3 | 2E3_POR-236_TP2 | 2F2_POR-216_TP4 | 2H1_POR-69_TP2 | 2H2_POR-216_TP1 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cluster_27 | 456 | 1436 | 1 | 301 | 163 | 21 | 0 | 95 | 4904 | 1 | 70 | 119 | 2590 | 1391 | 759 | 8 | 484 | 3162 | 41 | 5934 | 3894 | 285 | 664 | 3862 | 37 | 139 | 31 | 62 | 0 | 1125 | 2249 | 0 | 990 | 0 | 1 | 0 | 1459 |
| Cluster_491 | 90 | 301 | 0 | 565 | 50 | 5 | 0 | 55 | 1507 | 0 | 12 | 124 | 2370 | 429 | 660 | 6 | 300 | 1416 | 19 | 1653 | 869 | 107 | 264 | 1452 | 17 | 86 | 21 | 45 | 0 | 1104 | 766 | 0 | 1177 | 0 | 2 | 0 | 1243 |
| Cluster_661 | 7577 | 5129 | 4 | 4481 | 1440 | 113 | 0 | 3805 | 72664 | 5 | 173 | 239 | 98732 | 6002 | 5436 | 43 | 9308 | 194341 | 388 | 56469 | 21428 | 2500 | 67803 | 58565 | 754 | 2059 | 712 | 564 | 1 | 13887 | 23588 | 0 | 6607 | 0 | 3 | 0 | 11450 |
| Cluster_670 | 21 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 72 | 0 | 0 | 0 | 0 | 3 | 25 | 0 | 30 | 0 | 0 | 354 | 0 | 2 | 0 | 178 | 0 | 16 | 6 | 10 | 0 | 21 | 0 | 0 | 0 | 0 | 0 | 0 | 18 |
lncRNA
https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/E-Peve/output/12-Peve-lncRNA-discovery/lncRNA_counts.clean.filtered.txt Peve_lncRNA (first 4 rows)
| Geneid | Chr | Start | End | Strand | Length | POR-216-TP1 | POR-216-TP2 | POR-216-TP3 | POR-216-TP4 | POR-236-TP1 | POR-236-TP2 | POR-245-TP1 | POR-245-TP2 | POR-245-TP3 | POR-245-TP4 | POR-260-TP1 | POR-260-TP2 | POR-260-TP3 | POR-260-TP4 | POR-262-TP1 | POR-262-TP2 | POR-262-TP3 | POR-262-TP4 | POR-69-TP1 | POR-69-TP2 | POR-69-TP3 | POR-69-TP4 | POR-72-TP1 | POR-72-TP2 | POR-72-TP3 | POR-72-TP4 | POR-73-TP1 | POR-73-TP2 | POR-73-TP3 | POR-73-TP4 | POR-74-TP1 | POR-74-TP2 | POR-74-TP3 | POR-74-TP4 | POR-83-TP1 | POR-83-TP2 | POR-83-TP3 | POR-83-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| lncRNA_008 | Porites_evermani_scaffold_1 | 673926 | 676113 | + | 2188 | 57 | 44.0 | 55 | 24 | 81 | 20 | 62.25 | 37.75 | 6.5 | 94.5 | 38.92 | 11.0 | 21.5 | 28.75 | 56.5 | 100.5 | 62.75 | 72.25 | 59.25 | 27.25 | 25.25 | 29.0 | 155.25 | 64.75 | 63.75 | 77.5 | 42 | 27 | 14.5 | 22.75 | 34.33 | 15.0 | 31.75 | 14.75 | 101.5 | 13.25 | 21.75 | 48.75 |
| lncRNA_009 | Porites_evermani_scaffold_1 | 673941 | 676113 | + | 2173 | 57 | 44.0 | 55 | 24 | 81 | 20 | 62.25 | 37.75 | 6.5 | 94.5 | 38.92 | 11.0 | 21.5 | 28.75 | 56.5 | 100.5 | 62.75 | 71.75 | 59.25 | 27.25 | 25.25 | 29.0 | 155.25 | 64.75 | 63.75 | 77.5 | 42 | 27 | 14.5 | 22.75 | 34.33 | 15.0 | 31.75 | 14.75 | 101.5 | 13.25 | 21.75 | 48.75 |
| lncRNA_010 | Porites_evermani_scaffold_1 | 673950 | 676113 | + | 2164 | 57 | 44.0 | 55 | 24 | 81 | 20 | 62.25 | 37.75 | 6.5 | 94.5 | 38.92 | 11.0 | 21.5 | 28.75 | 56.5 | 100.5 | 62.75 | 71.75 | 59.25 | 27.25 | 25.25 | 29.0 | 155.25 | 64.75 | 63.75 | 77.5 | 42 | 27 | 14.5 | 22.75 | 34.33 | 15.0 | 31.75 | 14.75 | 101.5 | 13.25 | 21.75 | 48.75 |
| lncRNA_011 | Porites_evermani_scaffold_1 | 703501 | 725784 | + | 22284 | 9435 | 1153.5 | 369 | 690 | 833 | 362 | 4372.50 | 346.50 | 249.5 | 306.0 | 2273.17 | 243.5 | 1397.0 | 1631.50 | 1419.0 | 596.5 | 852.00 | 682.00 | 5023.00 | 828.00 | 103.50 | 1254.5 | 973.00 | 4401.50 | 526.50 | 7395.0 | 74 | 1307 | 203.5 | 3759.50 | 3442.83 | 1018.5 | 744.00 | 4214.50 | 995.5 | 8153.00 | 69.50 | 4554.50 |
mCpG Percentage
https://gannet.fish.washington.edu/metacarcinus/E5/Pevermanni/20250821_meth_Peve/merged-WGBS-CpG-counts_filtered_n20.csv Peve_mCpG (first 4 rows)
| CpG | POR-216-TP4 | POR-245-TP2 | POR-73-TP3 | POR-69-TP1 | POR-216-TP3 | POR-74-TP3 | POR-69-TP2 | POR-83-TP2 | POR-73-TP4 | POR-260-TP2 | POR-216-TP2 | POR-72-TP2 | POR-236-TP2 | POR-260-TP3 | POR-72-TP1 | POR-262-TP2 | POR-236-TP1 | POR-72-TP4 | POR-262-TP1 | POR-245-TP1 | POR-69-TP4 | POR-83-TP4 | POR-83-TP3 | POR-216-TP1 | POR-72-TP3 | POR-245-TP3 | POR-260-TP4 | POR-74-TP2 | POR-260-TP1 | POR-74-TP4 | POR-245-TP4 | POR-69-TP3 | POR-74-TP1 | POR-73-TP1 | POR-83-TP1 | POR-262-TP3 | POR-262-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CpG_Porites_evermani_scaffold_1000_100536 | 0 | NA | NA | NA | 0.000000 | NA | NA | NA | 0 | 0 | NA | 0 | NA | 0 | NA | 0 | NA | 0 | 0 | NA | 0 | NA | NA | 0 | NA | 0 | 0 | NA | 0 | NA | 0 | 10 | NA | 0 | 0 | 0 | 0 |
| CpG_Porites_evermani_scaffold_1000_100742 | 0 | NA | 0 | 0 | 0.000000 | NA | NA | NA | 0 | NA | 0 | NA | 0 | 0 | 0 | 0 | 0 | NA | NA | 0 | 0 | NA | 0 | NA | NA | 0 | 0 | NA | NA | 0 | NA | 0 | NA | 0 | NA | 0 | 0 |
| CpG_Porites_evermani_scaffold_1000_100744 | 0 | NA | 0 | 0 | 0.000000 | NA | 0 | NA | 0 | NA | 0 | NA | 0 | 0 | 0 | 0 | 0 | NA | NA | 0 | 0 | NA | 0 | NA | NA | 0 | 0 | NA | NA | 0 | NA | 0 | NA | 0 | NA | 0 | 0 |
| CpG_Porites_evermani_scaffold_1000_100776 | 0 | NA | 0 | 0 | 6.666667 | NA | NA | NA | 0 | NA | 0 | NA | NA | 0 | 0 | 0 | 0 | 0 | NA | NA | 0 | NA | NA | NA | NA | 0 | 0 | NA | NA | 0 | 0 | 0 | NA | 0 | NA | 0 | 0 |
Pocillopora tuahiniensis
Gene
https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/02.20-F-Ptua-RNAseq-alignment-HiSat2/ptua-gene_count_matrix.csv Ptuh_gene (first 4 rows)
| gene_id | POC-201-TP1 | POC-201-TP2 | POC-201-TP3 | POC-219-TP1 | POC-219-TP2 | POC-219-TP3 | POC-219-TP4 | POC-222-TP1 | POC-222-TP2 | POC-222-TP3 | POC-222-TP4 | POC-255-TP1 | POC-255-TP2 | POC-255-TP3 | POC-255-TP4 | POC-259-TP1 | POC-259-TP2 | POC-259-TP3 | POC-259-TP4 | POC-40-TP1 | POC-40-TP2 | POC-40-TP3 | POC-40-TP4 | POC-42-TP1 | POC-42-TP2 | POC-42-TP3 | POC-42-TP4 | POC-52-TP1 | POC-52-TP2 | POC-52-TP3 | POC-52-TP4 | POC-53-TP1 | POC-53-TP2 | POC-53-TP3 | POC-53-TP4 | POC-57-TP1 | POC-57-TP2 | POC-57-TP3 | POC-57-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| gene-Pocillopora_meandrina_HIv1___RNAseq.g20905.t1 | 54 | 170 | 18 | 168 | 31 | 11 | 70 | 296 | 51 | 388 | 33 | 72 | 84 | 36 | 65 | 294 | 226 | 47 | 140 | 60 | 7 | 56 | 47 | 42 | 31 | 28 | 0 | 0 | 52 | 99 | 157 | 84 | 39 | 162 | 61 | 17 | 51 | 177 | 206 |
| gene-Pocillopora_meandrina_HIv1___RNAseq.g20902.t1 | 957 | 759 | 143 | 757 | 446 | 96 | 399 | 664 | 304 | 1627 | 521 | 385 | 432 | 248 | 847 | 722 | 969 | 559 | 900 | 384 | 323 | 715 | 473 | 537 | 519 | 338 | 43 | 61 | 517 | 835 | 1374 | 831 | 439 | 1084 | 481 | 545 | 234 | 921 | 899 |
| gene-Pocillopora_meandrina_HIv1___RNAseq.g20903.t1 | 249 | 452 | 381 | 501 | 218 | 120 | 289 | 240 | 229 | 482 | 223 | 106 | 250 | 811 | 506 | 571 | 341 | 603 | 446 | 150 | 120 | 273 | 166 | 185 | 107 | 115 | 249 | 284 | 167 | 341 | 467 | 320 | 154 | 393 | 209 | 287 | 235 | 502 | 415 |
| gene-Pocillopora_meandrina_HIv1___TS.g25664.t1 | 365 | 191 | 13 | 73 | 64 | 0 | 110 | 719 | 186 | 215 | 111 | 489 | 118 | 0 | 98 | 109 | 287 | 91 | 109 | 259 | 215 | 114 | 420 | 370 | 521 | 275 | 23 | 46 | 216 | 76 | 100 | 111 | 180 | 183 | 139 | 305 | 96 | 88 | 274 |
Epigenetic Machinery
https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/F-Ptua/output/07-Ptua-epimachine-exp/Ptua-epimachine-expression.csv Ptuh_epimachine (first 4 rows)
| gene_id | protein_match | POC-201-TP1 | POC-201-TP2 | POC-201-TP3 | POC-219-TP1 | POC-219-TP2 | POC-219-TP3 | POC-219-TP4 | POC-222-TP1 | POC-222-TP2 | POC-222-TP3 | POC-222-TP4 | POC-255-TP1 | POC-255-TP2 | POC-255-TP3 | POC-255-TP4 | POC-259-TP1 | POC-259-TP2 | POC-259-TP3 | POC-259-TP4 | POC-40-TP1 | POC-40-TP2 | POC-40-TP3 | POC-40-TP4 | POC-42-TP1 | POC-42-TP2 | POC-42-TP3 | POC-42-TP4 | POC-52-TP1 | POC-52-TP2 | POC-52-TP3 | POC-52-TP4 | POC-53-TP1 | POC-53-TP2 | POC-53-TP3 | POC-53-TP4 | POC-57-TP1 | POC-57-TP2 | POC-57-TP3 | POC-57-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| gene-Pocillopora_meandrina_HIv1___RNAseq.22127_t | TRMT112-206 | 67 | 112 | 31 | 160 | 89 | 15 | 129 | 284 | 75 | 177 | 93 | 128 | 30 | 73 | 78 | 112 | 131 | 85 | 102 | 34 | 58 | 80 | 86 | 91 | 130 | 74 | 103 | 0 | 45 | 86 | 62 | 58 | 29 | 102 | 157 | 113 | 51 | 61 | 169 |
| gene-Pocillopora_meandrina_HIv1___RNAseq.26310_t | ADARB1-201 | 365 | 678 | 104 | 315 | 229 | 44 | 177 | 554 | 334 | 552 | 182 | 297 | 233 | 45 | 257 | 319 | 681 | 145 | 384 | 365 | 248 | 321 | 270 | 353 | 536 | 323 | 83 | 56 | 382 | 203 | 331 | 259 | 281 | 446 | 365 | 431 | 184 | 319 | 515 |
| gene-Pocillopora_meandrina_HIv1___RNAseq.6732_t | NAA50-201 | 581 | 548 | 133 | 343 | 251 | 118 | 315 | 482 | 342 | 641 | 372 | 337 | 349 | 230 | 376 | 253 | 637 | 521 | 671 | 333 | 521 | 598 | 403 | 454 | 739 | 446 | 210 | 91 | 601 | 408 | 442 | 334 | 383 | 547 | 391 | 760 | 393 | 667 | 1101 |
| gene-Pocillopora_meandrina_HIv1___RNAseq.g10407.t1 | Prdm16-206 | 182 | 185 | 55 | 225 | 40 | 50 | 30 | 598 | 94 | 790 | 88 | 225 | 59 | 87 | 111 | 175 | 135 | 60 | 92 | 35 | 27 | 105 | 25 | 33 | 21 | 49 | 0 | 72 | 42 | 154 | 259 | 195 | 83 | 333 | 47 | 66 | 57 | 272 | 50 |
miRNA
https://raw.githubusercontent.com/urol-e5/timeseries_molecular/refs/heads/main/M-multi-species/output/10-format-miRNA-counts/Ptuh_miRNA_counts_formatted.txt Ptuh_mirna (first 4 rows)
| Name | 1A3_POC-255_TP1 | 1A4_POC-52_TP1 | 1A5_POC-53_TP3 | 1A6_POC-52_TP3 | 1B11_POC-40_TP1 | 1B12_POC-222_TP2 | 1B8_POC-201_TP1 | 1C1_POC-57_TP2 | 1C2_POC-222_TP4 | 1C3_POC-222_TP3 | 1C7_POC-52_TP4 | 1C8_POC-42_TP1 | 1C9_POC-222_TP1 | 1D11_POC-255_TP3 | 1E10_POC-40_TP2 | 1E11_POC-219_TP1 | 1E12_POC-255_TP4 | 1E4_POC-259_TP2 | 1E6_POC-40_TP3 | 1E8_POC-42_TP3 | 1F2_POC-259_TP4 | 1F5_POC-40_TP4 | 1F9_POC-52_TP2 | 1G11_POC-53_TP1 | 1G12_POC-219_TP4 | 1G2_POC-219_TP3 | 1G4_POC-57_TP3 | 1G6_POC-53_TP2 | 1G7_POC-42_TP4 | 1G8_POC-259_TP3 | 1G9_POC-259_TP1 | 1H10_POC-201_TP2 | 1H4_POC-42_TP2 | 1H5_POC-201_TP3 | 1H9_POC-53_TP4 | 2A1_POC-219_TP2 | 2A2_POC-255_TP2 | 2C3_POC-57_TP1 | 2G2_POC-57_TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cluster_4 | 337 | 0 | 7 | 32 | 45 | 150 | 20 | 120 | 6 | 61 | 27 | 10 | 110 | 4 | 202 | 8 | 26 | 151 | 84 | 27 | 93 | 180 | 164 | 28 | 2 | 2 | 43 | 216 | 111 | 5 | 99 | 70 | 101 | 2 | 3 | 44 | 177 | 46 | 13 |
| Cluster_20 | 7176 | 3 | 236 | 588 | 273 | 1068 | 538 | 279 | 57 | 283 | 705 | 158 | 497 | 74 | 2069 | 50 | 526 | 3183 | 1046 | 254 | 1269 | 2788 | 2038 | 134 | 33 | 10 | 438 | 1186 | 804 | 96 | 2313 | 1182 | 743 | 80 | 48 | 200 | 2244 | 453 | 304 |
| Cluster_321 | 5942 | 2 | 240 | 1321 | 363 | 2868 | 409 | 241 | 145 | 1080 | 1113 | 540 | 1101 | 57 | 2924 | 26 | 433 | 2402 | 1237 | 1543 | 1699 | 3449 | 2527 | 131 | 33 | 8 | 495 | 1801 | 2954 | 43 | 2438 | 675 | 2335 | 112 | 83 | 133 | 1611 | 440 | 336 |
| Cluster_372 | 95668 | 26 | 1418 | 10524 | 3534 | 25828 | 3490 | 1867 | 1619 | 7821 | 9029 | 4128 | 20138 | 474 | 31324 | 507 | 5391 | 20852 | 12483 | 6715 | 8709 | 46907 | 22344 | 2315 | 186 | 47 | 5764 | 8602 | 34435 | 576 | 20214 | 6451 | 30983 | 712 | 293 | 2291 | 28434 | 8040 | 3467 |
lncRNA
https://raw.githubusercontent.com/urol-e5/timeseries_molecular/refs/heads/main/F-Ptua/output/06-Ptua-lncRNA-discovery/lncRNA_counts.clean.filtered.txt Ptuh_lncRNA (first 4 rows)
| Geneid | Chr | Start | End | Strand | Length | POC-201-TP1 | POC-201-TP2 | POC-201-TP3 | POC-219-TP1 | POC-219-TP2 | POC-219-TP3 | POC-219-TP4 | POC-222-TP1 | POC-222-TP2 | POC-222-TP3 | POC-222-TP4 | POC-255-TP1 | POC-255-TP2 | POC-255-TP3 | POC-255-TP4 | POC-259-TP1 | POC-259-TP2 | POC-259-TP3 | POC-259-TP4 | POC-40-TP1 | POC-40-TP2 | POC-40-TP3 | POC-40-TP4 | POC-42-TP1 | POC-42-TP2 | POC-42-TP3 | POC-42-TP4 | POC-52-TP1 | POC-52-TP2 | POC-52-TP3 | POC-52-TP4 | POC-53-TP1 | POC-53-TP2 | POC-53-TP3 | POC-53-TP4 | POC-57-TP1 | POC-57-TP2 | POC-57-TP3 | POC-57-TP4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| lncRNA_001 | Pocillopora_meandrina_HIv1___Sc0000000 | 130008 | 130966 | + | 959 | 115.00 | 241.0 | 118.0 | 230.0 | 154.0 | 22.0 | 118.0 | 175.0 | 122 | 209.0 | 176.0 | 86.0 | 191.00 | 207.0 | 217.00 | 225.00 | 199.00 | 171 | 215.0 | 58 | 94.0 | 168.0 | 55.00 | 145.0 | 93.0 | 108.0 | 41.0 | 12.0 | 106.0 | 150.0 | 170.00 | 195.00 | 117.00 | 196.0 | 109.00 | 186.00 | 112.0 | 230.00 | 136 |
| lncRNA_003 | Pocillopora_meandrina_HIv1___Sc0000000 | 163979 | 165466 | + | 1488 | 134.25 | 137.5 | 26.0 | 68.5 | 36.5 | 3.5 | 79.0 | 185.0 | 182 | 125.5 | 82.5 | 183.5 | 56.50 | 49.0 | 44.50 | 66.50 | 98.50 | 65 | 60.5 | 254 | 295.0 | 31.0 | 266.00 | 150.5 | 237.0 | 232.5 | 71.5 | 21.5 | 219.5 | 40.5 | 74.50 | 53.50 | 155.00 | 57.0 | 208.50 | 148.50 | 121.5 | 76.50 | 251 |
| lncRNA_004 | Pocillopora_meandrina_HIv1___Sc0000000 | 164651 | 165466 | + | 816 | 68.25 | 71.5 | 23.0 | 42.5 | 22.5 | 3.5 | 29.0 | 94.0 | 76 | 65.5 | 25.5 | 76.5 | 16.50 | 37.0 | 23.50 | 42.50 | 57.50 | 41 | 46.5 | 118 | 108.0 | 22.0 | 146.00 | 47.5 | 103.0 | 105.5 | 63.5 | 5.5 | 100.5 | 30.5 | 37.50 | 33.50 | 79.00 | 43.0 | 93.50 | 75.50 | 46.5 | 49.50 | 86 |
| lncRNA_005 | Pocillopora_meandrina_HIv1___Sc0000000 | 168862 | 182546 | + | 13685 | 107.75 | 141.0 | 57.5 | 80.5 | 55.5 | 8.5 | 44.5 | 111.5 | 115 | 100.0 | 122.0 | 171.0 | 115.33 | 76.5 | 144.33 | 231.33 | 184.83 | 96 | 124.0 | 59 | 36.5 | 78.5 | 80.83 | 26.0 | 51.5 | 41.0 | 39.0 | 11.5 | 75.5 | 75.0 | 148.33 | 159.67 | 113.17 | 100.5 | 100.33 | 78.67 | 89.5 | 92.33 | 209 |
mCpG Percentage
https://gannet.fish.washington.edu/metacarcinus/E5/Ptuahiniensis/20250821_meth_Ptua/merged-WGBS-CpG-counts_filtered_n20.csv Ptuh_mCpG (first 4 rows)
| CpG | POC-259-TP1 | POC-53-TP1 | POC-222-TP1 | POC-42-TP2 | POC-40-TP4 | POC-52-TP4 | POC-40-TP3 | POC-53-TP3 | POC-52-TP1 | POC-219-TP3 | POC-222-TP3 | POC-219-TP4 | POC-53-TP2 | POC-222-TP4 | POC-40-TP2 | POC-57-TP3 | POC-57-TP2 | POC-40-TP1 | POC-201-TP1 | POC-42-TP4 | POC-52-TP3 | POC-52-TP2 | POC-201-TP2 | POC-255-TP1 | POC-255-TP3 | POC-259-TP2 | POC-57-TP4 | POC-255-TP2 | POC-219-TP2 | POC-219-TP1 | POC-53-TP4 | POC-57-TP1 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CpG_Pocillopora_meandrina_HIv1___Sc0000000_1000005 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.000000 | 0 | 0 | 0 | 0 | 0 | 0 | NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.000000 | 0 | 0 | 0 | 0.00 |
| CpG_Pocillopora_meandrina_HIv1___Sc0000000_1000074 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | NA | 0.000000 | NA | 0 | NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.000000 | 0 | NA | 0 | 6.25 |
| CpG_Pocillopora_meandrina_HIv1___Sc0000000_1000090 | 0 | 0 | 0 | 0 | 10 | NA | 0 | 0 | 0 | NA | 5.555556 | 0 | 0 | NA | 0 | 0 | NA | 0 | 0 | NA | 0 | 0 | 0 | 0 | NA | 0 | 0 | 7.142857 | 0 | 0 | NA | 0.00 |
| CpG_Pocillopora_meandrina_HIv1___Sc0000000_1000108 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | NA | 0.000000 | 0 | 0 | NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | NA | 0 | 0 | NA | 0 | 0 | 0.000000 | 0 | 0 | 0 | 0.00 |