|
| Status |
Public on Mar 28, 2013 |
| Title |
kidney - MethylC-seq |
| Sample type |
SRA |
| |
|
| Source name |
kidney (4 year-old male)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
Sex: male
|
| Biomaterial provider |
NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, Baltimore, MD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue DNA was purified using Qiagen's Puregene kit. The genomic DNA was sonicated to ~300 bp and methylated Illumina adapters were ligated to the ends. 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurboCx Hotstart DNA Polymerase (Stratagene) for 14 cycles using Illumina's standard amplification protocol.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Reads were aligned to the genome using BS Seeker.
76 bp reads were processed with BS Seeker parameters -e 75 -m 2.
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%
Genome_build: hg18
Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site
|
| |
|
| Submission date |
Jul 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Janine LaSalle |
| E-mail(s) |
jmlasalle@ucdavis.edu
|
| Organization name |
UC Davis
|
| Street address |
Medical Microbiology and Immunology
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE39775 |
Examination of four human tissue samples by MethylC-seq |
| GSE39777 |
Comparison of DNA methylation in human tissues |
|
| Relations |
| SRA |
SRX172464 |
| BioSample |
SAMN01096251 |
