 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 30, 2022 |
| Title |
Control-29 |
| Sample type |
SRA |
| |
|
| Source name |
Blood, control
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Control
tissue: blood
Sex: male
age: 0.67
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from all donors using Magbead Blood DNA Kit (CWBIOTech, CW2361S) according to the manufacturer’s methods.
Products were purified using Agencourt AMPure XP beads (Beckman, p/n A63880) after sequencing library were constructed, the mitochondrial genome were captured with AI-Mito-Cap Kit (iGeneTech, Beijing, China) and sequenced on Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA) with 150 base paired‐end reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The sequence signatures with adapter ligation, low quality, and containing the unknown base > 5 were removed to obtain clean sequences.
The clean sequences were aligned to the human reference genome (UCSC hg19) by Burrows-Wheeler Aligner, and the alignment results were saved in BAM format files.
Further advanced analysis for the final BAM files, single nucleotide polymorphisms (SNPs) are detected by GATK and Insertion and Deletions (InDels) are detected by SAMtools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files.
|
| |
|
| Submission date |
Sep 04, 2019 |
| Last update date |
Aug 30, 2022 |
| Contact name |
Yueying Xiang |
| E-mail(s) |
[email protected]
|
| Organization name |
shenzhen university
|
| Department |
Shenzhen University General Hospital health management center
|
| Street address |
1098 Xueyuan Avenue, Nanshan District,Shenzhen 518000,China
|
| City |
shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE136892 |
Mitochondrial DNA atlas reveals physiopathology of type 2 diabetes |
|
| Relations |
| BioSample |
SAMN12696370 |
| SRA |
SRX6803095 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4061280_Control-29.txt.gz |
1.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
