|
| Status |
Public on Sep 05, 2019 |
| Title |
Chimpanzee Bone WGBS |
| Sample type |
SRA |
| |
|
| Source name |
Bone
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: Bone
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from bones using QIAamp® DNA Investigator kit (56504, Qiagen). Bones were cut to thin slices (0.2-0.5 mm) and then thoroughly washed (X5) with PBS, to clean samples from blood. Bones were crushed with mortar and pestle in liquid nitrogen and 100 mg bone powder was taken to extract DNA according to the protocol "Isolation of Total DNA from Bones and Teeth" of the DNA Investigator kit.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
WGBS
Whole-genome bisulfite sequencing (WGBS) was done on DNA extracted from a chimpanzee skull.
|
| Data processing |
Sequence quality was evaluated using FastQC software v0.11.2. TRIMMOMATIC v.0-32 was used to filter low quality bases with the following parameters: -phred33 LEADING:30 TRAILING:30 MAXINFO:70:0.9 MINLEN:70. Paired-end sequencing reads were mapped to bisulfite converted human or chimpanzee (hg19, panTro4) reference genome using Bismark v0.14.3 and bowtie2 v2.2.4 not allowing multiple alignments and using the following parameters: --bowtie2 --non_bs_mm --old_flag -p 4. Potential PCR duplicates were removed using Bismark’s deduplicate_bismark_alignment_output.pl Perl program. Bismark’s bismark_methylation_extractor script was used to produce methylation calls with the following parameters: -p --no_overlap --comprehensive --merge_non_CpG --no_header --bedGraph --multicore 2 --cytosine_report. Examination of the M-bias plots led us to ignore the first 5 bp of both reads in human samples. Custom scripts were used to summarize methylation levels at CpG sites based on the frequencies of methylated and unmethylated mapped reads on both strands.
Genome_build: panTro4 (Pan_troglodytes-2.1.4)
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
May 23, 2017 |
| Last update date |
Sep 05, 2019 |
| Contact name |
David Gokhman |
| E-mail(s) |
david.gokhman@mail.huji.ac.il
|
| Organization name |
The Hebrew University of Jerusalem
|
| Street address |
Givat Ram, Safra Campus
|
| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16809 |
| Series (1) |
| GSE96833 |
Archaic and modern bone DNA methylation maps from the Neanderthal, Denisovan, modern human and chimpanzee |
|
| Relations |
| BioSample |
SAMN07160079 |
| SRA |
SRX2847134 |
