|
| Status |
Public on Jun 25, 2019 |
| Title |
1515G |
| Sample type |
SRA |
| |
|
| Source name |
Brain BA46
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
brain region: Brodmann Area 46 (BA46)
subject id: 1515
age: 50
disease state: Schizo
Sex: female
|
| Treatment protocol |
Human post-mortem brain tissue from the Brodmann Area 46 (BA46) was obtained.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from 1mg to 5mg of tissue sample, using the Qiagen DNeasy Blood and Tissue DNA extraction kit according to manufacturer’s instructions. The extracted DNA was suspended in TE buffer and quantified by Qubit (Thermo Fisher Scientific).
Libraries were made with In-House Illumina sequencer compatible protocol. The extracted DNA was fragmented by S-series focused ultrasonicator (Covaris) using the “200bp-target peak size protocol”. Fragmented DNA was then size selected (200bp-600bp) with Agencourt aMPure XP bead-based (Beckman Coulter Cat. No. A63880) size selection protocol (Mark. A. Urich et al. 2015). The DNA End repair step was performed with End-It DNA end repair kit (Epicentre, Cat. No. ER81050. After End repair step, A-tailing (NEB, cat. No. M0202) and Ligation steps are performed to ligate methylated adaptors.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
54samples_ALLchr_biallelic_MAF005_HWE001_GENO005_PASS.fam
54samples_ALLchr_biallelic_MAF005_HWE001_GENO005_PASS.bed
54samples_ALLchr_biallelic_MAF005_HWE001_GENO005_PASS.bim
|
| Data processing |
Library strategy: Whole-genome sequencing
Quality and adapter trimming of raw reads was performed using TrimGalore (Babraham Institute). Reads were mapped to the human GRCh37 reference genome using BWA (version 0.7.4) and duplicates were removed using picard (version 2.8.3).
We identified genetic polymorphism from re-sequencing data following GATK v3.7 best practices workflow (McKenna, et al. 2010). We used HapMap 3.3, Omni 2.5M, 1000 Genomes Phase I and dbSNP 138 as training datasets for variant recalibration. We filtered variant calls with high genotype quality (GQ >=20.0).
We kept variants with genotype missingness below 5%, Hardy-Weinberg equilibrium test P>0.001 and minor allele frequency above 5%. The total genotyping rate was >0.99 and the maximum per individual missingness was 0.1%.
Genome_build: GRCh37
Supplementary_files_format_and_content: plink files
|
| |
|
| Submission date |
Dec 14, 2017 |
| Last update date |
Nov 08, 2019 |
| Contact name |
Soojin V Yi |
| E-mail(s) |
soojinyi@gatech.edu
|
| Organization name |
Georgia Institute of Technology
|
| Department |
School of Biology
|
| Street address |
950 Atlantic Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30318 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE108065 |
Genome-wide sequencing of schizophrenia and control individuals [WGS] |
| GSE108066 |
Contribution of differential cell-specific methylation to schizophrenia |
|
| Relations |
| SRA |
SRX3470801 |
| BioSample |
SAMN13245220 |
