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Status |
Public on Aug 14, 2019 |
Title |
ESCs, WT_ChIP_H3K9me3_rep2 |
Sample type |
SRA |
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Source name |
embryonic stem cell
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Organism |
Mus musculus |
Characteristics |
cell line: E14 chip antibody: H3K9me3 (C15500003, Diagenode) genotype: wild type
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Growth protocol |
E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 20% FBS, GlutaMAX (Gibco), MEM Non-Essential Amino Acids (Gibco), Leukemia inhibitory factor, 1 mM sodium pyruvate, penicillin/streptomycin, 0.1 mM 2-mercaptoethanol, 3 mM CHIR99021 and 1 mM PD0325901. Cells were cultured at 37 °C under 5% CO2 in air.
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Extracted molecule |
genomic DNA |
Extraction protocol |
For ChIP-seq, cells were fixed in 1% formaldehyde for 10 min at RT, and followed by glycine for 5 mins. Chromatin was sonicated to 200-500 bp, and immunoprecipitated with antibodies. Anti-mouse, rabbit IgG Dynabeads (Invitrogen) or StAv beads (Invitrogen) were added and incubated at 4°C. After washing the beads, beads-bound chromatin was tagemented by ChIPmentation strategy. Chromatin was eluted by reverse crosslink buffer at 65 ℃ for 12 hrs and purified with Monarch DNA Cleanup Columns. The libraries were prepared by using the Illumina Nextera DNA Library Prep Kit, and size-selected to 200-500 bp using SPRIselect beads.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 3000 |
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Data processing |
Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive. Non-uniquely mapping reads were filtered out using XS tag. PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools. Genome_build: mm10 Supplementary_files_format_and_content: bigWig file was generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY
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Submission date |
Aug 08, 2019 |
Last update date |
Aug 14, 2019 |
Contact name |
Misuzu Kurihara |
E-mail(s) |
kmisuzu1018@gmail.com, miyanari@nibb.ac.jp
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Organization name |
National Institute for Basic Biology
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Street address |
5-1 Higashiyama, Myodaiji
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City |
Okazaki |
State/province |
Aichi |
ZIP/Postal code |
444-8787 |
Country |
Japan |
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Platform ID |
GPL21493 |
Series (2) |
GSE135562 |
ChIP-seq analysis of wild-type and PML KO mESCs |
GSE135563 |
Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions |
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Relations |
BioSample |
SAMN12532178 |
SRA |
SRX6676109 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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