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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 12, 2018 |
| Title |
High throughput screen identifies novel small molecules that derepress genes repressed by DNA methylation |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
Genes repressed by DNA methylation can be derepressed by various compounds targeting DNA methyltransferases, histone deacetylases, etc. Here, we report a high throughput screen against a 308,251-member chemical library aiming to identify novel small molecules that derepress an EGFP reporter gene silenced by DNA methylation. RNA-seq was used to measure mRNA abundance in control and compound-treated cells.
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| Overall design |
RNA-seq was used to measure mRNA abundance in DMSO-treated cell, 5aza-dC treated cells, RG108-treated cells and 7 top hits novel compunds treated cells. MeDIP-seq was also done in untreated control cells.
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| Contributor(s) |
Li X, Shang E, Dong Q, Li Y, Zhang J, Xu S, Zhao Z, Shao W, Huang H, Zheng Y, Wang H, Lei X, Zhu B, Zhang Z |
| Citation(s) |
29559556 |
| Submission date |
Nov 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhuqiang Zhang |
| E-mail(s) |
zhangzhuqiang@ibp.ac.cn
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| Organization name |
Institute of Biophysics, CAS
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| Street address |
15 Datun Road, Chaoyang District.
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| City |
Beijing |
| State/province |
--- |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platforms (2) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA417267 |
| SRA |
SRP124263 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE106573_5azadC-treat-RNAseq-RPKM.txt.gz |
428.1 Kb |
(ftp)(http) |
TXT |
| GSE106573_DMSO-treat-RNAseq-RPKM.txt.gz |
423.1 Kb |
(ftp)(http) |
TXT |
| GSE106573_No1-compound-treat-RNAseq-RPKM.txt.gz |
426.4 Kb |
(ftp)(http) |
TXT |
| GSE106573_No2-compound-treat-RNAseq-RPKM.txt.gz |
423.7 Kb |
(ftp)(http) |
TXT |
| GSE106573_No3-compound-treat-RNAseq-RPKM.txt.gz |
425.6 Kb |
(ftp)(http) |
TXT |
| GSE106573_No4-compound-treat-RNAseq-RPKM.txt.gz |
424.5 Kb |
(ftp)(http) |
TXT |
| GSE106573_No5-compound-treat-RNAseq-RPKM.txt.gz |
426.1 Kb |
(ftp)(http) |
TXT |
| GSE106573_No6-compound-treat-RNAseq-RPKM.txt.gz |
424.9 Kb |
(ftp)(http) |
TXT |
| GSE106573_No7-compound-treat-RNAseq-RPKM.txt.gz |
423.8 Kb |
(ftp)(http) |
TXT |
| GSE106573_RAW.tar |
1.5 Gb |
(http)(custom) |
TAR (of BIGWIG) |
| GSE106573_RG108-treat-RNAseq-RPKM.txt.gz |
427.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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