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Sample GSM2881082

Query DataSets for GSM2881082

Status

Public on May 27, 2018

Title

reseq_jizi

Sample type

SRA

Source name

young panicle

Organism

Oryza sativa Japonica Group

Characteristics

cultivar: JZ1560
tissue: young panicle

Growth protocol

The rice seeds were germinated in sterilized water, and were then placed in soil in an experimental field of the Institute of Plant Physiology and Ecology (Shanghai, China) under natural growing conditions during kharif season of 2013. Panicles were harvested.

Extracted molecule

genomic DNA

Extraction protocol

Harvested samples were either frozen in liquid nitrogen for re-sequencing and RNA sequencing. or directly vacuum-infiltrated with formaldehyde cross-linking solution for ChIP assay. For rice samples, ChIP assay was performed with the antibody against H3 trimethyl-Lys 4 (Abcam, Cat. ab8580), H3 monomethyl-Lys 4 (Millipore,07-436), H3 trimethyl-Lys 27 (Upstate, USA, Cat. 07–449), H3 acetyl-Lys 27 (Upstate, USA, Cat. 07–360) and H3 trimethyl-Lys 36 (Abcam, Cat. ab9050)
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China). Libraries were sequenced on the HiSeq 2500 (Illumina) to produce 51 bp single reads for rice ChIP-seq, and 101 bp paired reads for re-sequencing and RNA sequencing.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2500

Description

Re-Sequencing

Data processing

The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to oryza sativa(MSU7.0) using bwa mem or tophat2 to map with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, macs 1.3 was used to identify read enriched regions(peaks). For RNA-Seq, HTSeq-count was used to count the RNA-seq alignment files.
Genome_build: MSU 7.0
Supplementary_files_format_and_content: In ChIP-Seq, peak files was provided; In RNA-Seq, read counts for genes(MSU7.0) was provided.

Submission date

Dec 07, 2017

Last update date

May 27, 2018

Contact name

yijing zhang

E-mail(s)

zhangyijing@fudan.edu.cn

Organization name

Fudan University

Department

Biochemistry