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Sample GSM6576069 Query DataSets for GSM6576069
Status Public on Sep 15, 2022
Title ChIP-Seq_LL-ZT16-rep2
Sample type SRA
 
Source name mature leaf
Organism Oryza sativa Indica Group
Characteristics cultivar: Minghui 63
treatment: constant light (LL)
time-point: ZT16
tissue: mature leaf
chip antibody: H3K9ac (Abcam, AB10812)
Extracted molecule genomic DNA
Extraction protocol Rice tissues were crosslinked with 1% formaldehyde and quenched with 0.2 M glycine.
0.5 to 1g of the sample was ground into a fine powder in liquid nitrogen, the chromatin was fragmented into 200-600 bp by ultrasound processing using Bioruptor (Diagenode). The lysates were incubated at 4 °C for 1 to 6 h and rotated to form antibody-bead complexes. After reverse cross-linking of DNA and protein, ChIP-DNA was extracted using phenol: chloroform: isoamyl alcohol (P3803; Sigma-Aldrich). ChIP-DNA libraries were prepared by Illumina® (New England BioLabs, E7645) using the NEBNext® Ultra™ II DNA Library Preparation Kit. AMPure XP beads (Beckman, A63881) were used to select 250-650 bp library fragments.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: bogWig file by deepTools bamCoverage
 
Submission date Sep 12, 2022
Last update date Sep 17, 2022
Contact name guoting chen
E-mail(s) chenguoting@webmail.hzau.edu.cn
Phone +86 13212791520
Organization name National Key Laboratory of Crop Genetic Improvement
Street address 1 Shizishan Street, Hongshan District
City Wuhan
ZIP/Postal code 430000
Country China
 
Platform ID GPL26667
Series (2)
GSE213226 Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]
GSE213227 Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice
Relations
BioSample SAMN30815497
SRA SRX17539465

Supplementary file Size Download File type/resource
GSM6576069_ChIP-Seq_LL-ZT16-rep2.bw 27.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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