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 39 40 40 39
Porites evermanni 38 38 37 38 37
Pocillopora tuahiniensis 39 39 39 39 32

Acropora pulchra

Gene

Download 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

Download Epigenetic Machinery

 https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/D-Apul/output/36-Apul-epimachine-counts/Apul-epimachine-expression.csv 

Apul_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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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

Download 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