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GEO help: Mouse over screen elements for information. |
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Status |
Public on Apr 29, 2023 |
Title |
ChIPseq_ESC_wt_H3K23ac_Unt_r2 |
Sample type |
SRA |
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Source name |
embryonic stem cells
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Organism |
Mus musculus |
Characteristics |
cell type: embryonic stem cells genotype: wild type strain: 129S6/SvEvTac treatment condition: basal p53 chip antibody: Active motif, H3K23ac 39131
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Treatment protocol |
Cells (1.5x10^7) were seeded into 15 cm plates the day before the experiment. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for 22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75ug of chromatin was used per IP, (3) protein A magnetic Dynabeads (Thermo Fisher Scientific) were used.
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Growth protocol |
Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human primary cell line (HMEC) were cultured in Mammary Epithelial Cell Growth Medium (Gibco MEGM) supplemented with growth factors (Gibco MEGM-SingleQuots CC-4136) BPE, hydrocortisone, hEGF, insulin and gentamicin/amphotericin-B (37°C, 7% CO2).
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Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was purified by Phenol:Chloroform extraction. Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10/hg19 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads. Assembly: mm10/hg19 Supplementary files format and content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and setting shift to 80. The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library.
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Submission date |
Apr 11, 2022 |
Last update date |
May 01, 2023 |
Contact name |
Luke Thomas Isbel |
E-mail(s) |
luke.isbel@adelaide.edu.au
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Organization name |
SAiGENCI
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Lab |
Isbel
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Street address |
4 North Terrace, AHMS, Lvl 9
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City |
Adelaide |
State/province |
South Australia |
ZIP/Postal code |
5000 |
Country |
Australia |
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Platform ID |
GPL17021 |
Series (2) |
GSE200580 |
Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner [ChIP-seq] |
GSE200586 |
Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner |
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Relations |
BioSample |
SAMN27517224 |
SRA |
SRX14812477 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6038046_ChIPseq_ESC_wt_H3K23ac_Unt_r2.wig.gz |
10.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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