|
| Status |
Public on Jan 27, 2019 |
| Title |
APO_2 |
| Sample type |
SRA |
| |
|
| Source name |
MKN45
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MKN45
cell type: adenocarcinoma, poorly differentiated
treatment: Apocynin 100μM treated
|
| Treatment protocol |
MKN45 cells were treated by Apocynin (100mM) or ethanol (control). After 3days, another aliquot of Apocynin was added. Total mRNA was extracted at day4.
|
| Growth protocol |
MKN45 cells were cultured in RPMI1640 medium with 1% N-2 supplement, 2% B27 (without vitaminA), 20 ng/ml bFGF and 100ng/ml EGF. They were cultured as spheres by using ultra low attachment plates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using ISOGEN (Nippon Gene) and purified using Rneasy Mini Kit (Quiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
polyA RNA
StrandNGS_Apocynin_MKN45_sphere.xlsx
|
| Data processing |
HiSeq Control Software (HCS) v2.2.58 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using StrandNGS.
The raw counts of each gene in a reference gene annotation (hg19) were calculated using the StrandNGS software, and were subjected to base 2 logarithmic conversion.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample
|
| |
|
| Submission date |
Mar 07, 2018 |
| Last update date |
Jan 27, 2019 |
| Contact name |
masanobu oshima |
| E-mail(s) |
oshimam@staff.kanazawa-u.ac.jp
|
| Organization name |
kanazawa university
|
| Street address |
Kakuma-machi
|
| City |
kanazawa |
| ZIP/Postal code |
920-1164 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE111520 |
mRNA sequence Analysis of Apocynin treated MKN45 |
|
| Relations |
| BioSample |
SAMN08647215 |
| SRA |
SRX3771763 |
