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| Status |
Public on Apr 23, 2019 |
| Title |
An siRNA screen identifies CHD4 as a target for epigenetic therapy |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
AIM: We performed RNA-sequencing experiments seeking genes whose expression changed after siCHD4 treatment.
METHOD: We generated cDNA libraries from RNA purified from SW48 treated by siNegative control, siCHD4, siNegative control plus siDNMT1, siCHD4 plus siDNMT1, siCHD4 plus Decitabine and siNegative control plus Decitabine. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the human genome hg19 using TopHat
RESULTS: We were able to map 23600 genes. 284 genes in siCHD4, 289 genes in siDNMT1, 309 genes in DAC, 1090 genes in siCHD4 plus siDNMT1 and 468 genes in siCHD4 plus siDNMT1 were significantly upregulated at least two fold compared to siNegative control.
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| Overall design |
We generated cDNA libraries from RNA purified from SW48 treated by siNegative control, siCHD4, siNegative control plus siDNMT1, siCHD4 plus siDNMT1, siCHD4 plus Decitabine and siNegative control plus Decitabine
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| Contributor(s) |
Cesaroni M, Okamoto Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
yasuyuki okamoto |
| E-mail(s) |
tue81852@temple.edu
|
| Organization name |
temple university
|
| Department |
fels
|
| Lab |
ISSA lab
|
| Street address |
3307 N. Broad Street
|
| City |
Philadelphia |
| State/province |
pa |
| ZIP/Postal code |
19140 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (18)
|
|
| Relations |
| BioProject |
PRJNA265187 |
| SRA |
SRP049370 |
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