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Sample GSM501691 Query DataSets for GSM501691
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

Supplementary file Size Download File type/resource
GSM501691_ChIP_p53_R1.bed.gz 49.9 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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