| 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: 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 |
| alexmendozasoler@gmail.com | |
| 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 |
| Relations | |
| 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 |