|
| Status |
Public on Sep 20, 2019 |
| Title |
1D n/Entr |
| Sample type |
SRA |
| |
|
| Source name |
dermal fibroblast cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
cell type: dermal fibroblast cells
|
| Treatment protocol |
The HDF cells were directly exposed to ultrasound stimulus (20 KHz, 1.0 W/cm2) for 5 sec. And then, 2 x 105 cells of ultrasound treated cells were cultured with ultrasound-treated media (20 KHz, 5.0 W/cm2, for 10min) on the 35mm petri dish.
|
| Growth protocol |
HDF cells were cultured with DMEM including 10% FBS, and 1% penicillin/streptomycin at 37 oC in an atmosphere of 5% CO2. Culture of hNSC was suspension cultured in StemPro® NSC SFM (Gibco) supplemented with 2 mM GlutaMAX™-I Supplement (Gibco), 6 U/mL heparin (Sigma-Aldrich, St. Louis, MO, USA), and 200 µM ascorbic acid (Sigma) at 37 oC in an atmosphere of 5% CO2. And n/Entr cells were cultured with ultrasound treated hNSC culture medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1ug of gDNA was sheared to 200~400bp using the Covaris LE220 sonicator (Covaris Inc. Woburn, MA). The fragmented products were immunoprecipitated using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) following the manufacture’s recommended protocol. Briefly, Methylated DNA was isolated from fragmented whole genomic DNA by binding to the methyl-CpG binding domain of human MBD2 protein, which is coupled to paramagnetic Dynabeads® M-280 Streptavidin via a biotin linker. The methylated fragments were eluted as a single enriched population with a 2000 mM NaCl elution buffer.
DNA libraries were prepared for sequencing using MethylMiner Methylated DNA Enrichment Kit (Invitrogen).
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate methylation levels, the MBD Seq reads were mapped to the genome of Homo sapiens(hg19) using Bowtie 1.1.1.
PCR duplicates were removed with Picard Mark Duplicates (version 1.118).
Raw data (the reads for mapped in genome) were normalized by RMS (Relative Methylayion Score) each ROI region using MEDIPS package (version 1.16.0).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited table includes RMS values for each Sample and ROI
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
Sep 20, 2019 |
| Contact name |
Yong Seung Lee |
| E-mail(s) |
inyasio0731@gmail.com
|
| Phone |
+82-32-290-2778
|
| Organization name |
Catholic Kwandong University
|
| Department |
College of Medicine
|
| Street address |
SimGokro 100gil 25
|
| City |
Incheon Metropolitan City |
| ZIP/Postal code |
404-834 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE87204 |
Ultrasound-mediated ultra effective cellular reprogramming of human fibroblasts into neural progenitor-like cells [MBD-Seq] |
| GSE87205 |
Ultrasound-mediated ultra effective cellular reprogramming of human fibroblasts into neural progenitor-like cells |
|
| Relations |
| BioSample |
SAMN05804813 |
| SRA |
SRX2185041 |
