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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 02, 2019 |
| Title |
plX_HALO_NRF_ampDAPseq |
| 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 AquNRF 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 and amplified 11 cycles, next it was incubated with in-vitro translated AquNRF 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 |
RL1410
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| Data processing |
Library strategy: ampDAP-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 |
SAMN10611003 |
| SRA |
SRX5157055 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3518752_plX_HALO_NRF_ampDAPseq_B_peaks.txt.gz |
44.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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