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Sample GSM1868525

Query DataSets for GSM1868525

Status

Public on May 13, 2016

Title

MIM396

Sample type

SRA

Source name

The panicles (secondary branch development stage)

Organism

Oryza sativa

Characteristics

genotype/variation: p35S:MIM396

Extracted molecule

total RNA

Extraction protocol

For ChIP, Lysates were clarified from sonicated nuclei and OsGRF6-DNA complexes were isolated with antibody. For RNA-seq, total RNAs were extracted with Trizol according to manufacturer’s manual.
For ChIP-Seq library construction, cross-linked chromatin was fragmented into 150-300bp, and then fragmented DNA was used for library construction and sequencing by Illumina Hiseq2000. RNA-Seq library construction was performed by using Illumina TruSeq kit

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Sequence reads for ChIP-Seq is 100bp paired-end and quality control was performed by Fastqc, and then low quality reads and adaptor contamination were deleted. For downstream analysis, data were mapped to Release 7 of the Michigan State University Rice Genome using Bowtie and MACS for peaks calling.
For RNA-Seq, the clean reads were mapped to the rice genome using the Cufflink software. Gene expression was calculated according to the fragments per kilobase of exon per Million fragments mapped (FPKM) method.
Genome_build: MSU rice genome 7.0
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each RNA-Seq data. Tab-delimited text file include peaks location for ChIP-Seq data.

Submission date

Sep 03, 2015

Last update date

May 15, 2019

Contact name

Wang Kun

Organization name

wuhan university

Street address

Ba-yi Road

City

Wuhan