|
| Status |
Public on Dec 31, 2022 |
| Title |
skate_st31_pelvic_fin_MethylCseq |
| Sample type |
SRA |
| |
|
| Source name |
little skate stage 31 embryonic pelvic fin DNA subjected to MethylC-seq
|
| Organism |
Leucoraja erinaceus |
| Characteristics |
age: stage 31 embryo
tissue type: pelvic fin
|
| Treatment protocol |
no treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MethylC-seq library preparation was performed as described previously (PMID: 25692984). Briefly, 1000 ng of genomic DNA extracted from embryonic and adult skate fins was spiked with unmethylated λ phage DNA (Promega) and sonicated to ~300 bp fragments using M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA was then purified, end-repaired using End-It™ DNA End-Repair Kit (Lucigen) and A-tailed using Klenow Fragment (3'→5' exo-) (New England Biolabs) followed by the ligation of NEXTFLEX® Bisulfite-Seq Adapters. Bisulfite conversion of adaptor-ligated DNA was performed using EZ DNA Methylation-Gold Kit (Zymo Research). Library amplification (13 PCR cycles) was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems). Library size was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche) yielding ~10-20 nM.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads in fastq format were trimmed using Trimmomatic software (ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:50)
Trimmed reads were mapped to Leri_hhj.fasta genome reference (containing the λ phage genome as chrLambda) using WALT (Chen et al, 2016) with the following settings: -m 10 -t 24 -N 10000000 -L 2000.
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true (http://broadinstitute.github.io/picard/).
The numbers of methylated and unmethylated cytosines at each genomic CpG position were called using the MethylDackel extract genome.fasta input.bam -o output --mergeContext. Genotype and methylation bias correction were performed using MethylDackel (MethylDackel extract Leri_hhj_lambda.fasta $input_bam -o $output --mergeContext --minOppositeDepth 5 --maxVariantFrac 0.5 --OT 10,110,10,110 --OB 40,140,40,140) (https://github.com/dpryan79/MethylDackel). (https://github.com/dpryan79/MethylDackel)
Genome_build: little skate: Leri_hhj.fasta
Supplementary_files_format_and_content: bedGraph / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting hydroxymethylated bases; 6. The number of alignments/pairs reporting unmethylated bases
|
| |
|
| Submission date |
Dec 12, 2021 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Ksenia Skvortsova |
| E-mail(s) |
k.skvortsova@garvan.org.au
|
| Phone |
478135210
|
| Organization name |
Garvan Institute
|
| Department |
Genomics and Epigenetics
|
| Lab |
Developmental Epigenomics
|
| Street address |
384 Victoria St, Darlinghurst
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL31064 |
| Series (1) |
| GSE190730 |
Base-resolution DNA methylation maps of little skate (Leucoraja erinacea) |
|
| Relations |
| BioSample |
SAMN23958216 |
| SRA |
SRX13388737 |
