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Sample GSM4017186 Query DataSets for GSM4017186
Status Public on Aug 14, 2019
Title ESCs, PmlKO_ChIP_H3K4me3_rep1
Sample type SRA
 
Source name embryonic stem cell
Organism Mus musculus
Characteristics cell line: E14
chip antibody: H3K4me3 (MABI0304, Cosmo Bio)
genotype: Pml-/-
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.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
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
 
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
Organization name National Institute for Basic Biology
Street address 5-1 Higashiyama, Myodaiji
City Okazaki
State/province Aichi
ZIP/Postal code 444-8787
Country Japan
 
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
Relations
BioSample SAMN12532169
SRA SRX6676102

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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