|
| Status |
Public on Nov 04, 2015 |
| Title |
H2AXS139ph_Chip_seq_in_MEF_Hmga2_Ko |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblast (MEF)
|
| Organism |
Mus musculus |
| Characteristics |
cells: Mouse Embryonic Fibroblast (MEF)
embryo stage: E15.5
passages: 2_to_4
strain: C57BL/6
genotype/variation: Hmga2 Ko
chip antibody: H2AXS139ph (Millipore, cat: 05-636, lot 2019732)
|
| Growth protocol |
MEF cells were kept at 37°c in DMEM medium containing 10 % Fetal Calf Serum, and 1% P/S/G (penicillin/Streptomycin/L-glutamine)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated chromatin and Protein-DNA complexes were isolated with the antibody.
Libraries were prepared according to Illumina's instructions accompanying the Ovation Ultra Low Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
H2AXS139ph_Chip_seq_in_MEF_Hmga2_Ko_raw_data
Processed data description: contig file to use for ngs.plot use; to see the enrichment of H2AXS139ph in wt and ko Hmga2 MEF samples in the promoter region
Processed data file: 01_contigs_H2AXS139ph_in_Hmga2_MEF_wt_vs_H2AXS139ph_in_Hmga2_MEF_Ko.txt
|
| Data processing |
Visualization of raw reads was done using FASTX-ToolKit, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min lemgh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files were merge using bamtools merge (default)
MACS14 was used for the peak calling 4 (p < 0.01) with a shiftsize of 30 bp
homer makeUCSC (normalized to 30 millions) was used to obtain bedgraph files to Visualize in UCSC genome browser
ngsplot was used to obtain the Normalized Taq (log2) to the promoter area of Wt samples of H2AXS139ph and ATM compared to Ko samples
homer annotatepeaks was used to perform the taq density ofHMGA2, H2AXS139ph, and ATM to the peaks of HMGA2 in Wt samples
Genome_build: mm10
Supplementary_files_format_and_content: bed files obtained after MACS14, promoter files from H2AXS139ph and ATM obtained after annotation of peaks files by the location on promoter using homer annotatepeak
Supplementary_files_format_and_content: [H2AXS139ph_and_ATM_in_Hmga2_MEF_wt_compared_HMGA2_in_MEF_Hmga2_wt_peaks.txt] this Text file is the output file obtained after using homer annotatePeaks.pl ; it is a quantitative file considered relevant for the context of the project
Supplementary_files_format_and_content: [01_contigs_H2AXS139ph_in_Hmga2_MEF_wt_vs_H2AXS139ph_in_Hmga2_MEF_Ko.txt] it is a text file that is required for ngs.plot (program to visualize Chip-sea data) , needed to reproduce the figure of the manuscript
Supplementary_files_format_and_content: [01_contigs_ATM_in_Hmga2_MEF_wt_vs_ATM_in_Hmga2_MEF_ko_in_promoter_wt.txt] it is a text file that is required for ngs.plot , needed to reproduce the figure of the manuscript
|
| |
|
| Submission date |
Dec 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Guillermo Barreto |
| E-mail(s) |
guillermo.barreto@univ-lorraine.fr
|
| Organization name |
CNRS Director of Research
|
| Department |
Campus Biologie-Santé. Faculté de Médecine
|
| Lab |
Laboratoire IMoPA. UMR 7365 CNRS
|
| Street address |
9, Avenue de la Forêt de Haye ‐ BP 20199
|
| City |
Nancy Cedex |
| ZIP/Postal code |
54505 |
| Country |
France |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE63861 |
High Mobility Group protein mediated transcription requires DNA damage marker γ-H2AX |
|
| Relations |
| BioSample |
SAMN03252929 |
| SRA |
SRX796322 |
