GSM8189874: WT_H3_rep2, ChIP-seq; Oryza sativa Japonica Group; ChIP-S... - SRA

SRX24173417: GSM8189874: WT_H3_rep2, ChIP-seq; Oryza sativa Japonica Group; ChIP-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 65.3M spots, 19.6G bases, 5.7Gb downloads

External Id: GSM8189874_r1

Submitted by: School of Life Science, Fudan University

Study: ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies

PRJNA935781 • SRP423049 • All experiments • All runs

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To investigate the effect of the OsINO80, we analysed OsINO80 binding regions and analysed genome-wide H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 in the mutant and WT by ChIP-seq. Overall design: ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies.

Sample: WT_H3_rep2, ChIP-seq

SAMN40786209 • SRS20949481 • All experiments • All runs

Organism: Oryza sativa Japonica Group

Library:

Name: GSM8189874

Instrument: Illumina NovaSeq 6000

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: PAIRED

Construction protocol: Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail. The ChIP-seq libraries were constructed by following the manufacturer's instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

Runs: 1 run, 65.3M spots, 19.6G bases, 5.7Gb

Run	# of Spots	# of Bases	Size	Published
SRR28573859	65,302,998	19.6G	5.7Gb	2024-04-10

ID:: 32484391

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