|Status||Public on Apr 11, 2018|
|Source name||2 weeks culture|
|Organism||Klebsormidium flaccidum (Klebsormidium nitens)|
|Growth protocol||BCDAT medium, 23º, continuous light|
|Extracted molecule||genomic DNA|
|Extraction protocol||DNeasy Plant Mini kit (Cat. No. 69104, Qiagen)
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 4 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).
|Instrument model||Illumina HiSeq 1500|
|Data processing|| CASAVA v1.8.2
For methylC-seq, adapters were trimmed with BBduk with the options mink=3, qtrim=r, trimq=10 minlength=20, before alignment to the reference genome with Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.5.9 before methylation quantification with BSseeker2. For RNA-seq, reads were were aligned to the reference genome with HISAT2 --rna-strandness FR -N 1 --max-intronlen 20000 --dta, and a reference transcriptome was obtained using Stringtie default commands. Gene level expression quantification was obtained using Kallisto 0.42.3 using the annotation obtained from Stringtie and Augustus in intron-less mode (S_kawagutii_transcriptome.fasta.gz).
To build Symbiodinium minutum reference using BSseeker2, the scaffold names of the genome assembly were simplified using only the scaffold##### for each sequence entry, while the constant ".1|size####" were excluded.
Genome_build: Symbiodinium kawagutii assembly was downloaded from: http://web.malab.cn/symka_new/download.jsp, Symbiodinium minutum assembly was downloaded from http://marinegenomics.oist.jp/symb/viewer/download?project_id=21 ( symbB.v1.0.genome.fa.gz), Klebosrmidium nitens was downloaded from http://www.plantmorphogenesis.bio.titech.ac.jp/~algae_genome_project/klebsormidium/kf_download/120824_klebsormidium_Scaffolds_v1.0.fna (120824_klebsormidium_Scaffolds_v1.0.fna), Saccharomyces cerevisiae assembly was downloaded from NCBI (GCF_000146045.2_R64_genomic.fna.gz) Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome (2) nucleotide on Watson (+) strand (3) position (4) context (CG/CHG/CHH) (5) dinucleotide-context (CA/CC/CG/CT) (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here). Kallisto.tsv files contain target_id, length, effective length, estimated counts, tpm.
|Submission date||Oct 02, 2017|
|Last update date||Apr 11, 2018|
|Contact name||Alex de Mendoza|
|Organization name||The University of Western Australia|
|Street address||35 Stirling Highway|
|Series (1)||GSE104474 Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons|
|chromosome||context (CG/CHG/CHH)||position||context (CG/CHG/CHH)||dinucleotide-context (CA/CC/CG/CT)||methylation-level||#_of_C||= #_of_C + #_of_T|