The BS-seq data of Klebsormidium flaccidum

Status Public on Apr 11, 2018
Title mC_K_nitens
Sample type SRA
Source name 2 weeks culture
Organism Klebsormidium flaccidum (Klebsormidium nitens)
Characteristics strain: NIES-2285
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).
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 1500
Description RL633
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:, Symbiodinium minutum assembly was downloaded from ( symbB.v1.0.genome.fa.gz), Klebosrmidium nitens was downloaded from (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 (, 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
Lab Lister Lab
Street address 35 Stirling Highway
City Perth
State/province Western Australia
ZIP/Postal code 6009
Country Australia
Platform ID GPL24069
Series (1) GSE104474 Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons
BioSample SAMN07728351
SRA SRX3236100

chromosome context (CG/CHG/CHH) position context (CG/CHG/CHH) dinucleotide-context (CA/CC/CG/CT) methylation-level #_of_C = #_of_C + #_of_T
chrL G 1 -- -- 0.0 0 1
chrL G 2 -- -- 0.0 0 3
chrL G 3 CHH CC 0.0 0 4
chrL C 4 CG CG 0.0 0 2
chrL G 5 CG CG 0.0 0 6
chrL G 6 CHG CC 0.0 0 7
chrL C 7 CG CG 0.0 0 2
chrL G 8 CG CG 0.0 0 9
chrL C 10 CHH CC 0.0 0 2
chrL C 11 CHH CT 0.0 0 2
download the file from here: download the data