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SRX6676101: GSM4017185: ESCs, WT_ChIP_H3K4me3_rep2; Mus musculus; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 72.7M spots, 2.6G bases, 912.5Mb downloads

Submitted by: NCBI (GEO)
Study: ChIP-seq analysis of wild-type and PML KO mESCs
show Abstracthide Abstract
Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate roles of PML bodies in transcriptional regulation, we conducted ChIP-seq analysis for histone modifications, including H3K4me3, H3K27ac, H3K27me3, and H3K9ac with wild-type and PML knockout mESCs. Overall design: Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive. Multiple mapped reads were filtered out using XS tag. PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools. BigWig files were generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY.
Sample: ESCs, WT_ChIP_H3K4me3_rep2
SAMN12532170 • SRS5234077 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 3000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction 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.
Experiment attributes:
GEO Accession: GSM4017185
Links:
Runs: 1 run, 72.7M spots, 2.6G bases, 912.5Mb
Run# of Spots# of BasesSizePublished
SRR992715672,709,0512.6G912.5Mb2019-08-14

ID:
8804767

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