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| Status |
Public on Aug 14, 2019 |
| Title |
ESCs, PmlKO_ChIP_H3K4me3_rep1 |
| 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: H3K4me3 (MABI0304, Cosmo Bio)
genotype: Pml-/-
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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 |
SAMN12532169 |
| SRA |
SRX6676102 |
| 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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