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| Status |
Public on Feb 27, 2021 |
| Title |
koala_WGBS_PC_brain |
| Sample type |
SRA |
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| Source name |
Right hemisphere cerebral lobe
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| Organism |
Phascolarctos cinereus |
| Characteristics |
Sex: female
australian museum registration: M.45022
tissue: brain
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
All genomic DNA was extracted using a Bioline Isolate II Genomic DNA Extraction Kit (Cat#. BIO-52067) following the recommended protocol with an additional DNAse free RNaseA (100mg/ml) (Qiagen cat. #19101) treatment before column purification.
The bisulfite conversion was carried out by using the EX DNA Methylation-Lightning Kit (Zymo cat. #D5030) and the WGBS libraries were constructed using the TruSeq DNA methylation kit (Illumina cat.# EGMK81213).
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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 |
Paired-end raw fastq files were processed for quality control and adapter trimming using Trim Galore! (version 0.3.7) with a Phred score threshold of 20. To remove contaminating reads, the trimmed reads were mapped to the phi-X174 (NC_001422.1) reference assembly with Bismark version 0.18.1 using Bowtie 2 (Krueger and Andrews 2011) and only unmapped reads were retained for downstream analyses.
Final QC reads were then mapped to the koala reference assembly (phaCin_unsw_v4.1; (Johnson, et al. 2018)) using Bismark with the Bowtie 2 setting.
Two sequencing runs were performed per tissue sample which were merged following the read mapping step. All merged mapped files were deduplicated using Bismark’s deduplicate_bismark
Reports containing per-CpG-site methylation calls were subsequently generated using bismark_methylation_extractor, bismark2bedGraph, and coverage2cytosine in series for each sample.
Genome_build: phaCin_unsw_v4.1
Supplementary_files_format_and_content: Bismark cytosine report tab-delimited text files including chromosome, position, strand, methylated read count, unmethylated read count, cytosine context, and trinucleotide context
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| Submission date |
Apr 29, 2020 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Devika Singh |
| Organization name |
Georgia Institute of Technology
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| Street address |
North Ave NW
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| City |
ATLANTA |
| State/province |
Georgia |
| ZIP/Postal code |
30332 |
| Country |
USA |
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| Platform ID |
GPL26281 |
| Series (1) |
| GSE149600 |
Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation |
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| Relations |
| BioSample |
SAMN14771362 |
| SRA |
SRX8207654 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4505500_WGM145_01_S1_brain_PC_CpG_report.txt.gz |
174.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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