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Status |
Public on Aug 02, 2019 |
Title |
plX_HALO_EGR_DBD_DAPseq |
Sample type |
SRA |
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Source name |
swimming_larva_0h
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Organism |
Amphimedon queenslandica |
Characteristics |
developmental stage: swimming_larva_0h individuals: individuals from Heron Island experimental variable: incubated with in-vitro translated AquEGR DNA binding domain fused to HaloTag
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Extracted molecule |
genomic DNA |
Extraction protocol |
Phenol-chloroform extraction Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquEGR DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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Description |
RL1404
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Data processing |
Library strategy: DAP-seq CASAVA v1.8.2 For Bisulfite-seq and TAB-seq, 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.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 166679601". Genome_build: Amphimedon queenslandica genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/amphimedon_queenslandica/dna/Amphimedon_queenslandica.Aqu1.dna.toplevel.fa.gz, Sycon ciliatum genome assembly was downloaded from http://www.compagen.org/datasets/SCIL_WGA_130802.zip, Nematostella vectensis genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/nematostella_vectensis/dna/Nematostella_vectensis.ASM20922v1.dna.toplevel.fa.gz, Mnemiopsis leidyi genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/mnemiopsis_leidyi/dna/Mnemiopsis_leidyi.MneLei_Aug2011.dna.toplevel.fa.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 sum of reads showing C or T in that position). Macs2 xls files are described in https://github.com/taoliu/MACS/blob/master/README.rst.
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Submission date |
Dec 18, 2018 |
Last update date |
Aug 03, 2019 |
Contact name |
Alex de Mendoza |
E-mail(s) |
alexmendozasoler@gmail.com
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Organization name |
Queen Mary University of London
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Department |
School of Biological and Behavioural Sciences
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Lab |
de Mendoza Lab
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Street address |
Mile End Road. Fogg Building 5.14
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City |
London |
ZIP/Postal code |
E1 4NS |
Country |
United Kingdom |
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Platform ID |
GPL22487 |
Series (1) |
GSE124016 |
Convergent evolution of a vertebrate-like methylome in a marine sponge |
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Relations |
BioSample |
SAMN10611153 |
SRA |
SRX5157050 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3518747_plX_HALO_EGR_DBD_DAPseq_B_peaks.txt.gz |
353.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data provided as supplementary file |
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