|
Status |
Public on Mar 01, 2011 |
Title |
p53_ChIPSeq_replicate1 |
Sample type |
SRA |
|
|
Source name |
p53 Saos-2 cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: Saos-2 cell type: osteosarcoma antibody: DO1 against p53 genetic modification: Tet-on FLp53
|
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 |
Chromatin IP against p53
|
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 |
SRX016979 |
BioSample |
SAMN00009030 |