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| Status |
Public on Aug 15, 2018 |
| Title |
gut_rep2_RRBS |
| Sample type |
SRA |
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| Source name |
gut
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| Organism |
Branchiostoma lanceolatum |
| Characteristics |
developmental stage: adult
tissue: gut
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Adult tissues were homogenized in 3 volumes STOP buffer (15 mM EDTA, 10 mM Tris-HCl pH7.5, 1% SDS, 0.5 mg/mL proteinase K) after which two phenol:chloroform:isoamylalcohol (PCI, 25:24:1) extractions were performed. DNA was then precipitated in 1/5 volume NH4AC 4M and 3 volumes EtOH and dissolved in 100 uL, treated with RNase and purified by a PCI extraction. The precipitation was done with EtOH and the DNA was resuspended in 50 uL H2O.
RRBS library generation was performed as described previously (Murphy et al, 2018; Cell). Briefly, 125ng of genomic DNA was digested using MspI restriction enzyme. Digested DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Bisulphite conversion of adapter-ligated DNA fragments was performed using EZ DNA Methylation-Gold Kit. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 11 cycles of amplification.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
HiSeq X Ten |
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| Description |
gut2
Amphioxus-gut_muscle_notochord_RRBS_CHH_bigtable.tsv; Amphioxus-gut_muscle_notochord_RRBS_CpG_bigtable.tsv
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| Data processing |
RRBS libraries were sequenced in paired-end mode on the Illumina HiSeqX platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome Branchiostoma lanceolatum (Bl71nemr) using WALT alignment algorithm and MethylDackel to extract cytosine methylation metrics with default parameters.
Genome_build: Branchiostoma lanceolatum: Bl71nemr
Supplementary_files_format_and_content: For "*_bigtable.tsv" processed data files the column headers are as follows: column 1 - assembly (chromosome). column 2 - position: coordinate for the cytosine position on the chromosome. columns 3, 5, 7, 9, 11, 13 (.C) - number of reads depicting a methylated cytosine. columns 4, 6, 8, 10, 12, 14 (.cov) - total number of reads at that position.
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| Submission date |
Jun 14, 2018 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Ozren Bogdanovic |
| E-mail(s) |
o.bogdanovic@gmail.com
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| Organization name |
Garvan Institute of Medical Research
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| Department |
Genomics and Epigenetics
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| Street address |
384 Victoria Street
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| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
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| Platform ID |
GPL25186 |
| Series (1) |
| GSE102144 |
Base resolution methylome profiling of Branchiostoma lanceolatum embryos and adult tissues |
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| Relations |
| BioSample |
SAMN09425940 |
| SRA |
SRX4216847 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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