|
| Status |
Public on Oct 01, 2015 |
| Title |
Exp1 C2 iMEFs Ezh2 -/-, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
C2 iMEFs Ezh2 -/-
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iMEFs
antibody: H3K27me3 ChIP (Active Motif 39155)
|
| Treatment protocol |
4-hydroxytamoxifen was used at a final concentration ranging from 1 nM to 1 μM
|
| Growth protocol |
Sample 1 to 16 iMEF cells grown in DMEM medium supplemented with 10% FCS, 100 mM non essential amino acids, 1 mM L-Glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by phenol-chloroform and precipitated. Experiment 1 : Sequencing was performed on SOLiD 5500 single reads 75bp. Experiment 2 : Sequencing was performed on Hi-Seq 2500 Illumina single reads 100bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Data processing |
Experiment 1 : Single-end reads were mapped on the Mouse reference genome (mm9) Using the Bowtie software (v0.12.8, Langmead B. Et al. 2012) Allowing one mismatch in the seed (28bp) And reporting one location in case of multiple mapping hits.
Experiment 1 : Peak calling for each sample was done with MACS2 2.0.10 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA as Control.
Experiment 2 : Single-end 100bp reads were mapped on the Mouse reference genome (mm9) Using the Bowtie2 software (v2.1.0, Langmead B. Et al. 2012) Allowing one mismatch in the seed (22bp) And reporting one location in case of multiple mapping hits.
Experiment 2 : PCR duplicates were then removed using samtools
Experiment 2 : Peak calling for each sample was done with CCAT 3.0 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA BAM file as Control.
Genome_build: mm9
Supplementary_files_format_and_content: bed files are the output of peak calling.
Supplementary_files_format_and_content: BigWig files are generated with HOMER (v3.17)
|
| |
|
| Submission date |
Jul 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
Nicolas.Servant@curie.fr
|
| Organization name |
Institut Curie
|
| Street address |
26 rue d'ulm
|
| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL16790 |
| Series (2) |
| GSE59293 |
Genome-wide analysis of H3K27me3 in Ezh2-conditional iMEFs |
| GSE59427 |
Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis |
|
| Relations |
| BioSample |
SAMN02911606 |
| SRA |
SRX652240 |
