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| Status |
Public on Oct 26, 2020 |
| Title |
mC_NeuralTube_amphioxus |
| Sample type |
SRA |
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| Source name |
Neural tube
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| Organism |
Branchiostoma lanceolatum |
| Characteristics |
source: Collected in Banyuls, France
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNeasy Blood & Tissue kit (Qiagen)
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 300 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).
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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 |
CASAVA v1.8.2
Adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.8 before methylation quantification with CGmaptools
Genome_build: Monodelphis domestica we used ENSEMBL Monodelphis_domestica.BROADO5.dna.toplevel.fa
Genome_build: Ornithorhynchus anatinus we used ENSEMBL Ornithorhynchus_anatinus.OANA5.dna.toplevel.fa
Genome_build: Gallus gallus we used ENSEMBL Gallus_gallus.Galgal4.dna.toplevel.fa
Genome_build: Callorhinchus milii we used calMil1 (GCA_000165045.2)
Genome_build: Lethenteron camtschaticum we used LetJap1.0 (GCA_000466285.1)
Genome_build: Apis mellifera we used ENSEMBL Apis_mellifera.GCA_000002195.1.31.dna.genome.fa
Genome_build: Octopus bimaculoides we used ENSEMBL Octopus_bimaculoides.PRJNA270931.dna.toplevel.fa
Genome_build: Branchiostoma lanceolatum we used ENSEMBL Branchiostoma_lanceolatum.BraLan2.dna.toplevel.fa
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2/CGmaptools (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 sum of reads showing C or T in that position).
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| Submission date |
Dec 06, 2019 |
| Last update date |
Oct 27, 2020 |
| Contact name |
Ryan Lister |
| E-mail(s) |
ryanlister@gmail.com
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| Phone |
61864884407
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| Organization name |
The University of Western Australia
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| Street address |
35 Stirling Highway
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| City |
Perth |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
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| Platform ID |
GPL27879 |
| Series (1) |
| GSE141609 |
Evolution of CpH methylation in vertebrate brains |
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| Relations |
| BioSample |
SAMN13508506 |
| SRA |
SRX7285999 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4209500_mC_NeuralTube_amphioxus.CGmap.gz |
710.4 Mb |
(ftp)(http) |
CGMAP |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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