GSM4082905: V2_H3K9me3; Dictyostelium discoideum; ChIP-Seq - SRA

SRX6862283: GSM4082905: V2_H3K9me3; Dictyostelium discoideum; ChIP-Seq
1 ILLUMINA (NextSeq 500) run: 19.6M spots, 1.5G bases, 614.2Mb downloads

Submitted by: NCBI (GEO)

Study: Determine the genome-wide localization of histone and histone marks in different stages of D. discoideum

PRJNA565992 • SRP222093 • All experiments • All runs

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We report the chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) on H3, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, and H3K36me3. ChIP-seq were sequenced to a depth of at least 8 million total reads/sample. We found that H3K4me3, H3K27ac and H3K4me1 show separation between unicellular and multicellular stages in principal component analysis (PCA); other marks were unable to show a clear separation in PCA. Overall design: Examine the localizaiton of histone marks and nucleosome postioning in D. discoideum (AX2) thorughout the genome

Sample: V2_H3K9me3

SAMN12775821 • SRS5400059 • All experiments • All runs

Organism: Dictyostelium discoideum

Library:

Instrument: NextSeq 500

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: 10 million D. discoideum cells were cross-linked with 1x linking buffer (11 mM HEPES-NaOH, 110 mM NaCl, 1.1 mM EDTA and 1.1 mM EGTA) with 1% formaldehyde for 10 minutes at RT and quenched by 2M glycine. The samples were fragmented by applying a biorupter for 25 cycles in the cold room with 30 seconds on and 30 seconds off per cycle. The precleared chromatin was incubated with antibody-coupled bead slurries and rotated at 4°C overnight. DNA was eluted from the beads by 200 µl TE with 1% SDS. Histone ChIP-Seq libraries were generated using the Ovation Ultralow V2 kit (Nugen, 0344-32) according to the manufacturer's instructions. Libraries were PCR amplified for 13-16 cycles depending on the antibody, and library quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Seventy-five bp reads were generated on the Illumina Nextseq 500 (Illumina). ChIP-seq were sequenced to a depth of at least 8 million total reads/sample.

Experiment attributes:

GEO Accession: GSM4082905

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 19.6M spots, 1.5G bases, 614.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR10133909	19,634,581	1.5G	614.2Mb	2021-04-21

ID:: 9030908

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