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Sample GSM2842841 Query DataSets for GSM2842841
Status Public on Mar 12, 2018
Title No4-compound-treat-RNAseq-rep1
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: No4-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
No4-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) zhangzhuqiang@ibp.ac.cn
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 SAMN07981683
SRA SRX3367311

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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