|
| Status |
Public on Sep 20, 2019 |
| Title |
p1 n/Entr |
| Sample type |
SRA |
| |
|
| Source name |
dermal fibroblast cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
passage: p7
|
| 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 |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol reagent. The construction of library was performed using SENSE 3’ mRNA-Seq Library Prep Kit from 1 ug of total RNA.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer v.0.0.14), then mapped to hg19 whole genome using tophat2 v.2.0.9
Read count were calculated using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Sep 09, 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 |
GPL18573 |
| Series (2) |
| GSE86644 |
Ultrasound-mediated ultra effective cellular reprogramming of human fibroblasts into neural progenitor-like cells [RNA-Seq] |
| GSE87205 |
Ultrasound-mediated ultra effective cellular reprogramming of human fibroblasts into neural progenitor-like cells |
|
| Relations |
| BioSample |
SAMN05757703 |
| SRA |
SRX2155407 |
