|
| Status |
Public on Aug 16, 2016 |
| Title |
Gibbon_S24 |
| Sample type |
SRA |
| |
|
| Source name |
Prefrontal Cortex
|
| Organism |
Hoolock leuconedys |
| Characteristics |
tissue: Prefrontal Cortex
age: 6years
|
| Treatment protocol |
We used the EpiTect Bisulfite Kits (Qiagen, Valencia, CA) to conduct bisulfite conversions of genomic DNA following the manufacturer's instructions. Sodium bisulfite converts unmethylated cytosine to uracil, which is then PCR amplified as thymidine and methylated cytosine remain cytosine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted according to the DNeasy Blood&Tissue Kit (QIAGEN) protocol.
DNA libraries were prepared for sequencing using Nextera XT DNA Sample Preparation protocol
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
pooling bisulfate PCR products from bis treated DNA that extracted from prefrontal cortex tissue
|
| Data processing |
Quality and adaptor trimming was performed using TrimGalore! with default parameters
Reads were mapped to the respective reference genomes (hg19, pantro4,rheMac3,macFas5 and nomLeu3) and methylation calling was done using Bismark with default parameters
Duplicates were removed using Bismark deduplication script with default parameters
Non-human species coordinates were converted to hg19 using UCSC liftover tool
Genome_build: hg19
Supplementary_files_format_and_content: Miseq_Methylated_Read_Count.txt file contains the number of methylated reads per CpG site and individual. Columns 1-3 show chromosome, start and end coordinates of each CpG, respectively. Columns 4-41 show number of methylated reads per sample
Supplementary_files_format_and_content: Miseq_Coverage_Read_Count.txt file contains the number reads per CpG site and individual. Columns 1-3 show chromosome, start and end coordinates of each CpG, respectively. Columns 4-41 show number of total reads per sample
|
| |
|
| Submission date |
Jan 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
lei shi |
| E-mail(s) |
shilei@mail.kiz.ac.cn
|
| Organization name |
Kunming Institute of Zoology
|
| Street address |
No.17 Longxin Road
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650201 |
| Country |
China |
| |
|
| Platform ID |
GPL21328 |
| Series (2) |
| GSE76788 |
Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [methylation] |
| GSE85868 |
Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution |
|
| Relations |
| BioSample |
SAMN04397512 |
| SRA |
SRX1528575 |
