|
| Status |
Public on Jan 06, 2014 |
| Title |
C02-HF_Bisulfite-seq |
| Sample type |
SRA |
| |
|
| Source name |
Hair follicle
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Hair follicle
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolation of genomic DNA by proteinase-k digestion and phenol-chloroform extraction.
Illumina libraries were generated according to the manufacturer’s sample preparation protocol for genomic DNA. Around 1ug of genomic DNA was fragmented to 200-500bp and end-repaired. The 5’ ends of DNA fragments were phosphorylated and a single adenine base was added to 3’ end. The Y-shape illumina adaptors were ligated to the genomic DNA. The bisulfite treated DNA was amplified by using adaptor-specific primers and fragments of 200-500 bp were isolated by bead purification. The quantity and size distribution of sequencing libraries were determined using the Pico Green fluorescence assay and the Agilent 2100 Bioanalyzer, respectively. The DNA was sequenced on the Illumina HiSeq 2000 as 100-bp paired-end reads, following the manufacturer's protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4 followed by adapter trimming by cutadapt program using default parameters. Adapter trimmed reads are mapped to hg19 genome build using BSMAP bisulfite-seq mapping software using default parameters and allowing 7 mismatches and methylation estimates of genome-wide CpG sites were obtained using in-house perl script.
Genome_build: hg19
Supplementary_files_format_and_content: text format with hg19 chromosome coordinates. Column1=chr;Column2=position;Column3=methylated reads;Column4=Total.no. of reads.
|
| |
|
| Submission date |
Mar 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Govindarajan Kunde Ramamoorthy |
| E-mail(s) |
RAMAMOOR@BCM.EDU
|
| Phone |
7137980349
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1100 Bates Street
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44806 |
Whole genome bisulfite-seq of two healthy males. |
|
| Relations |
| SRA |
SRX248435 |
| BioSample |
SAMN01974733 |
