|
| Status |
Public on Jun 12, 2018 |
| Title |
MKN74-mir1271-mimic3 |
| Sample type |
SRA |
| |
|
| Source name |
gastric cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
strain: MKN74
molecular subtype: total RNA
treatment: mir1271_mimic
|
| Treatment protocol |
Synthetic mimic of mir-1271 were purchased from the Thermo Fisher Scientific. 2×105 cells onto a 6-well plate (SPL) were transfected with 100 pmoles of miRNA using Lipofectamine® RNAiMAX (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MBD2-immunoprecipitated chromatin fragments were extracted for MBD-seq. RNAs were isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific)
We collected MBD2-immunoprecipitated chromatin fragments and genomic libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina).RNAs were isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific) and libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MKN74_mir1271
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Aug 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jong Hwan Kim |
| E-mail(s) |
kkjjhhk@kribb.re.kr
|
| Phone |
0821093299557
|
| Organization name |
Korea Research Institute of Bioscience and Biotechnology
|
| Department |
Genome structure research center
|
| Street address |
125 Gwahak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
ASI|KR|KS015|DAEJEON |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE87785 |
Sequencing-based analyses characterize a tumor suppressive role of mir-1271 repressed by DNA hypermethylation in gastric cancer |
|
| Relations |
| BioSample |
SAMN07448144 |
| SRA |
SRX3059809 |
