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| Status |
Public on Jun 04, 2012 |
| Title |
Input-seq in P19.6 cells |
| Sample type |
SRA |
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| Source name |
Untreated P19.6 cells, input
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| Organism |
Mus musculus |
| Characteristics |
cell line: P19.6
cell type: embryonal carcinoma cells
background strain: C3H/HeHa
treatment: none
ip antibody: none
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| Treatment protocol |
P19.6 cells were differentiated with 1 µM all-trans retinoic acid (RA) for 48 hours.
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| Growth protocol |
P19.6 mouse embryonal carcinoma cells were grown in high glucose Dulbeccos' Modified Eagle's Medium (DMEM) containing 10% fetal calf serum (GIBCO).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions by the IGBMC sequencing facility (Strasbourg, France). P19.6 cells were cross-linked with 1.5% formaldehyde for 10 min at room temperature. The cells were rinsed with cold PBS, harvested and lysed with 1% SDS, 10 mM EDTA, and 50 mM Tris-HCl (pH 8.1) containing a protease inhibitor cocktail (Roche). Chromatin fragmentation was subsequently obtained by sonicating samples for 14 min (30 sec on/off cycles) using a Bioruptor (Diagenode) set up at the highest intensity. The soluble chromatin was diluted 10 times in a buffer containing 1% Triton, 2 mM EDTA, 150 mM NaCl, and 20 mM Tris-HCl (pH 8.1), and incubated overnight with antibodies. Sepharose beads (Amersham Pharmacia Biosciences) were then added to the samples together with yeast tRNA as non-specific competitors. After 4 h, beads were serially washed using 1mL of washing buffer I (2mM EDTA, 20mM Tris-HCl (pH8.1), 0.1% SDS, 1% Triton X-100, 150mM NaCl), washing buffer II (2mM EDTA, 20mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 500 mM NaCl), washing buffer III (1mM EDTA, 10mM Tris-HCl (pH8.1), 1% NP-40, 1% deoxycholate, 0.25M LiCl) and then twice with 1mM EDTA, 10mM Tris-HCl (pH8.1), and immune complexes were eluted using 100 mL of 1% SDS and 0.1 M NaHCO3. Samples were incubated overnight at 65C to reverse cross-linking. DNA was finally purified using the NucleoSpin Extract II kit (Macherey-Nagel). Each ChIP was performed 10 times. The 10 samples were pooled and concentrated by DNA precipitation.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).
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| Data processing |
Reads were mapped to the reference genome (mouse mm8) by Bowtie (Langmead et al. Genome Biol. 2009 (PMID 19261174)). Mapped reads were processed by the MACS algorithm (Model-based Analysis of ChIP-Seq) (Zhang Y et al. Genome Biol. 2008 (PMID 18798982)).
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| Submission date |
Oct 24, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Aurelien Serandour |
| E-mail(s) |
aurelien.serandour@cruk.cam.ac.uk
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| Phone |
00441223769723
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| Organization name |
Université de Rennes 1
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| Department |
UMR CNRS 6290
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| Lab |
Equipe SP@RTE
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| Street address |
Bâtiment 13, Campus de Beaulieu
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| City |
Rennes |
| ZIP/Postal code |
35042 |
| Country |
France |
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| Platform ID |
GPL9250 |
| Series (2) |
| GSE27436 |
Dynamic hydroxymethylation of DNA marks differentiation-driven enhancers |
| GSE33067 |
Whole-genome mapping of MEIS1, TET1, H3K4me2 and H3K27ac in P19.6 mouse embryonal carcinoma cells and P19.6 cells treated for 48 hours with all-trans retinoic acid |
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| Relations |
| SRA |
SRX102949 |
| BioSample |
SAMN00744136 |
| Named Annotation |
GSM821509_P19_-RA_input_mm8.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM821509_P19_-RA_input_mm8.sam.gz |
1007.5 Mb |
(ftp)(http) |
SAM |
| GSM821509_P19_-RA_input_mm8.wig.gz |
38.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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