|
| Status |
Public on Aug 20, 2016 |
| Title |
gi-2_S24 |
| Sample type |
SRA |
| |
|
| Source name |
Prefrontal Cortex
|
| Organism |
Hoolock leuconedys |
| Characteristics |
tissue: Prefrontal Cortex
age: 6 years
|
| 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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Gibbon
PCR products mix
pooling PCR products from 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) with bwa
Duplicate reads were removed using Picard
Identified SNPs using GATK v3.4 and standard hard filtering parameters ("QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0").
Genome_build: hg19, pantro4,rheMac3,macFas5 and nomLeu3
Supplementary_files_format_and_content: vcf (variant format files)
|
| |
|
| Submission date |
Aug 19, 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) |
| GSE85867 |
Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [SNP] |
| GSE85868 |
Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution |
|
| Relations |
| SRA |
SRX2036216 |
| BioSample |
SAMN05597832 |
