|
Status |
Public on Sep 20, 2019 |
Title |
p5 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 |
SAMN05757710 |
SRA |
SRX2155408 |