|
| Status |
Public on Jan 30, 2008 |
| Title |
Transcriptome analyses of HeLa cells treated by CTCF RNAi(1) |
| Sample type |
RNA |
| |
|
| Source name |
HeLa cells treated by CTCF RNAi
|
| Organism |
Homo sapiens |
| Characteristics |
HeLa cells treated by CTCF RNAi was used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The siRNA oligos were annealed according to manufacturer’s instruction and used at a final concentration of 100-200 nM. The siRNA transfection was performed using oligofectamine (Invitrogen) and the cells were synchronized in G2 phase by double thymidine block before harvesting. For the preparation of total RNA from mammalian cells, Trizol extraction protocol was used, followed by a clean up step using the RNeasy Total RNA Isolation Mini Kit (Qiagen 74104).To minimize the possibility of artifacts by RNAi treatment, experiment was performed twice, using two different oligos for the knock down of hScc1 and CTCF, respectively.
|
| Label |
biotin
|
| Label protocol |
IVT labelling was performed using GeneChip Expression 3'-Amplification Reagents (P/N900449)
|
| |
|
| Hybridization protocol |
Samples were denatured at 99C for 5 minutes, and then put at 45C for 5min. before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).
|
| Scan protocol |
Arrays were scanned using the Genechip Scanner3000 7G following the library array description.
|
| Description |
Transcriptome analyses of HeLa cells treated by CTCF RNAi(1). CTCF RNAi sample was compared with non-treated control RNAi sample(ControlRNAi(1)).
|
| Data processing |
Chip data was analyzed by MAS (Microarray Analysis Suit) 5 software provided by Affymetrix using default setting.
|
| |
|
| Submission date |
Nov 16, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Katsuhiko Shirahige |
| E-mail(s) |
[email protected]
|
| Phone |
+81-3-5842-0756
|
| Fax |
+81-3-5842-0757
|
| URL |
http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/
|
| Organization name |
The University of Tokyo
|
| Department |
Research Center for Epigenetic Disease
|
| Lab |
Laboratory of Genome Structure and Function
|
| Street address |
1-1-1 Yayoi
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0032 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE9613 |
Cohesin mediates transcriptional insulation by CCCTC-binding factor |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
