|
| Status |
Public on Feb 04, 2020 |
| Title |
03_58 |
| Sample type |
SRA |
| |
|
| Source name |
cerebellum from deceased patient
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: control
tissue: cerebellum
age: 85
Sex: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN AllPrep DNA/RNA/miRNA Universal Kit protocol
Nugen Ovation RRBS Methyl-Seq protocol with QIAGEN EpiTech Fast DNA Bisulfite Kit for bisulfite conversion
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
bisulfite conversion
|
| Data processing |
NextSeq550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings. Reads were filtered for full-length(70bp) reads.
Fastq header contains 8 nt index sequence and N6 Nugen RRBS duplicate information. Adaptors and low quality reads were trimmed with Trim_galore v0.4.5. and reads containing adapter were discarded.
Following adaptor and quality trimming, the fastq files were further trimmed with NuGEN custom python script trimRRBSdiversityAdaptCustomers.py. Potential PCR or optical duplicates were removed using NuGEN python script Nudup.py
Trimmed reads was aligned to the human genome, allowing for 1 mismatch and retaining only uniquely mapped reads. Bam files were generated using Bismark v0.16.334. CpG coverage reports were generated using MethylKit from bam files.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: CpG coverage report in text format
|
| |
|
| Submission date |
Jul 17, 2019 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Charles Wang |
| E-mail(s) |
[email protected]
|
| Phone |
(909) 558-4325
|
| Organization name |
Loma Linda University
|
| Department |
Department of Basic Sciences
|
| Lab |
Center for Genomics
|
| Street address |
11021 Campus Street
|
| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92350 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE134426 |
Next Generation Sequencing Facilitated Cerebellum DNA Methylation Analysis of Essential Tremor Patients |
|
| Relations |
| SRA |
SRX6457344 |
| BioSample |
SAMN12307029 |
