|
| Status |
Public on Mar 01, 2011 |
| Title |
ChIP_Input_control |
| Sample type |
SRA |
| |
|
| Source name |
Saos-2 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Saos-2
cell type: osteosarcoma
antibody: none
genetic modification: None
|
| Treatment protocol |
To induce stable transfected TAp73beta and p53, 2.0 µg/mL of doxycyclin were used for 24 hr, for TAp73alpha induction 0.5 µg/mL were used
|
| Growth protocol |
The human osteosarcoma cell lines Saos-2 with inducible TAp73alpha, TAp73beta or p53 were maintained in Dulbecco modified Eagle medium supplemented with 10% fetal calf serum at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sonicated using a Bioruptor Sonicator.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Input
|
| Data processing |
35 bp reads were aligned to the human genome (hg18) using ELAND. Peaks were called using MACS with default settings and p-value threshold of 1e-5. Peaks files are available from the Series record.
|
| |
|
| Submission date |
Jan 27, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Marion Lohrum |
| E-mail(s) |
Lohrum@em.uni-frankfurt.de
|
| Phone |
+31 24 3610541
|
| Fax |
+31 24 3610520
|
| URL |
http://www.ncmls.nl/NCMLS/MenuStructures/PI/theme3/MarionLohrum.asp
|
| Organization name |
NCMLS
|
| Department |
Molecular Biology
|
| Street address |
P.O. Box 9101
|
| City |
Nijmegen |
| ZIP/Postal code |
6500 HB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE15780 |
Interplay between c-Jun and TAp73α/β contributes to the apoptosis-survival balance |
|
| Relations |
| SRA |
SRX016974 |
| BioSample |
SAMN00009025 |
