|
| Status |
Public on Mar 12, 2018 |
| Title |
No6-compound-treat-RNAseq-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK 293 transfected with reporter construct
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human embryonic kidney
cell line: HEK 293 transfected with reporter construct
treatment: No6-compound treated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were sythesised using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT.
MeDIP-seq were performed as previously described (Xiong et al, Molecular Cell 64, 913-925). Mouse monoclonal anti-5-methylcytidine (BI-MECY-000) for MeDIP was purchased from Eurogentec.
The MeDIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).
The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
somatic cell
No6-compound-treat-RNAseq-RPKM.txt.gz
|
| Data processing |
Basecalls performed by BGI, Shenzhen
Data were filtered using samtools rmdup to remove potential PCR duplicates
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantitified by Cuffdiff.
Genome_build: hg38 (RNA-seq)
Genome_build: hg19 (MeDIP-seq)
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 250 bp
|
| |
|
| Submission date |
Nov 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhuqiang Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Biophysics, CAS
|
| Street address |
15 Datun Road, Chaoyang District.
|
| City |
Beijing |
| State/province |
--- |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE106573 |
High throughput screen identifies novel small molecules that derepress genes repressed by DNA methylation |
|
| Relations |
| BioSample |
SAMN07981677 |
| SRA |
SRX3367316 |
