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| Status |
Public on Jan 15, 2024 |
| Title |
A. millepora adult 2 |
| Sample type |
SRA |
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| Source name |
Coral Fragment
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| Organism |
Acropora millepora |
| Characteristics |
tissue: Coral Fragment
protocol: whole genome bisulfite-seq
treatment: Parent
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| Growth protocol |
Specimens of A. millepora and A. selago were collected and placed into raceways 7 days before spawning. Sperm and egg were collected from each colony on the night of spawning and separated to be fertilized in controlled crosses. Larvae were kept at 27 °C for 5 days until larval development completed. After development, we fixed larvae from each successful cross in 100% Ethanol and stored at -80 °C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from adult corals and from individual and pooled larvae (approximately 10 larvae per pool). Samples were lysed through bead beating and 2-hour incubation with CTAB buffer at 65 °C. Subsequently, an organic DNA extraction is performed using phenol:chloroform:isoamyl alcohol (25:24:1). DNA was then cleaned using the Zymo Clean & Concentrate kit.
Whole genome bisulfite (WGBS) preparation was only completed on adult coral samples and pooled larvae using the Zymo-Seq WGBS Library Kit.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
WGBS reads trimmed with Trim Galore 0.6.7
Trimmed adult WGBS reads aligned to Amil v2.1 with Bismark v 0.24.2 with with mapping parameters -N 1 --score_min L,0,-0.8
md-RAD reads trimmed and aligned with Bowtie2 v. 2.5.0
Adult WGBS and md-RAD alignments variant called with ANGSD 0.940
Fixed SNP differences between adults were determine from variant calls, then used to create N-masked reference genomes for each pair of parents, with SNPsplit’s genome preparation script
Offspring WGBS files aligned to parent-specific masked genomes, using Bismark v 0.24.2.
Offspring alignments separated by parental alleles using SNPsplit v 0.6
Methylation calls extracted from adult WGBS alignments and offspring allele-specific alignments using Bismark’s methylation extraction script.
Assembly: Acroproa millepora, v2.1
Supplementary files format and content: Gzipped tab separated coverage file, created by Bismark’s methylation extraction script; Columns are: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary files format and content: Offspring have separate coverage files for each allele-specific alignment
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| Submission date |
Jan 10, 2024 |
| Last update date |
Jan 15, 2024 |
| Contact name |
Christopher Peterson |
| Organization name |
University of Texas
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| Department |
Integrative Biology
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| Street address |
2415 Speedway #C0930
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platform ID |
GPL33727 |
| Series (1) |
| GSE252970 |
Mixed patterns of intergenerational DNA methylation inheritance in Acropora |
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| Relations |
| BioSample |
SAMN39409428 |
| SRA |
SRX23168814 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8011663_lane1-A4-D_S4_L001_1.trim_bismark_bt2_pe.deduplicated.bismark.cov.gz |
144.1 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
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