|
| Status |
Public on Jun 12, 2018 |
| Title |
SNU484_MBDseq |
| Sample type |
SRA |
| |
|
| Source name |
gastric cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SNU484
tissue/cell type: gastric cancer cell line
molecular subtype: genomic DNA
|
| 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 |
genomic DNA |
| 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 |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SNU484
|
| Data processing |
RNA_seq;
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using Tophat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
miRNA-seq;
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using Tophat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
MBD_seq;
Base calling performed using CASAVA version 1.7
mapped to hg19 whole genome using bwa v.0.5.9
Methylation levels were called using pysam (-2 kb~500 bp from TSS). Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content:
RNA_seq; tab-delimited text files include FPKM values for each Sample
miRNA-seq; tab-delimited text files include RPKM values for each Sample
MBD_seq; bedgraph files were generated using homer
|
| |
|
| Submission date |
Oct 10, 2016 |
| 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 |
GPL11154 |
| Series (1) |
| GSE87785 |
Sequencing-based analyses characterize a tumor suppressive role of mir-1271 repressed by DNA hypermethylation in gastric cancer |
|
| Relations |
| BioSample |
SAMN05893094 |
| SRA |
SRX2235576 |
