|
| Status |
Public on Aug 28, 2018 |
| Title |
Mixed tPBAT Library - 9.6 fmol |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR-90
amount of input library: 9.6 fmol
cell type: fibroblast-like cell
tissue: lung
developmental stage: 16 week embryo
|
| Treatment protocol |
Cells were removed from culture flask with Tripsin-EDTA and collected by centrifugation.
|
| Growth protocol |
Cultured in MEM+10%FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified using QIAAmp Mini Kit
Genomic DNA was treated with bisufite using Methyl Easy Gold Kit from Zymo Research, then adaputor tagging was performed with tPBAT protocol.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Reads were mapped on mixed reference of human genome hg19 and lammbda phage genome using in-house program BMap.
Alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport
Genome_build: hg19 and lambra genome
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Aug 27, 2018 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Fumihito Miura |
| Organization name |
The University of Tokyo
|
| Department |
Graduate School of Frontier Sciences
|
| Street address |
Kashiwanoha 5-1-5
|
| City |
Kashiwa |
| State/province |
Chiba |
| ZIP/Postal code |
277-8562 |
| Country |
Japan |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE119068 |
Optimization of the input amount of library for whole-genome bisulfite sequencing on HiSeq X Ten |
|
| Relations |
| BioSample |
SAMN09917452 |
| SRA |
SRX4613706 |
