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Sample GSM3140225

Query DataSets for GSM3140225

Status

Public on Sep 14, 2018

Title

WT ChIP rep1

Sample type

SRA

Source name

Kernel

Organism

Zea mays

Characteristics

strain: B73
tissue: Endosperm
age: 15 DAP

Treatment protocol

N/A

Growth protocol

Plants were grown under greenhouse conditions (16-h day) at the University of Arizona during June to October 2012, and self-pollinated to obtain 15-DAP kernels.

Extracted molecule

genomic DNA

Extraction protocol

RNA was isolated from dissected endosperms using an SDS-phenol method. ChIP was performed using the ChIP Assay Kit (Millipore Corporation, Billerica, MA) by following the manufacturer’s instruction with modifications.
Using a TruSeq DNA Sample Preparation Kit v2 (Illumina), poly(A)-containing mRNAs were purified, fragmented, and reverse-transcribed by the Univ. Arizona Genetics Core facility to construct multiplexed RNA-Seq libraries. Using an Illumina Pico DNA Seq Library Preparation Kit (Gnomegen Inc.), nearly 10 ng of purified ChIPed DNA from each endosperm sample (2 genotypes × 2 replicates) was used by the Univ. Arizona Genetics Core facility to generate a set of multiplexed ChIP-Seq libraries by following the manufacturer’s instruction.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Description

chromatin DNA
O2_peaks.txt.gz

Data processing

Illumina HiSeq 2500
Raw reads from RNA-Seq and ChIP-Seq were trimmed to remove adapter sequences and low-quality bases using the Trimmomatic program with the parameter TRAILING set to three. The resulting RNA-Seq reads were mapped to the maize reference genome using Tophat v2.0.9. Reads mapped to each gene were counted using the multicov function of BEDTools v2.17.0 and normalized using the R package edgeR v3.2.4 with the trimmed mean of M-values method. The genes with raw counts per million (CPM) > 1 in at least 3 samples were tested for differential expression analysis using edgeR with an exact test analogous to Fisher’s exact test. FDR < 0.05 was used as the cutoff to call DEGs. The trimmed ChIP-Seq reads were mapped to the reference genome using Bowtie v2.1.0 with the following parameters: --score-Min L, -0.6, -0.18 --end-to-end --very-sensitive --no-discordant. Mapped reads for duplicates of the B73 samples and the B73o2 samples (control) were merged, respectively, and were used for peak-calling using MACS v2.1.0.20140616 with the following parameters: -g 2.06e9 -q 0.01 -mfold 10 30.
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: A tab-delimited text file containing RPKM normalized using edgeR, and a tab-delimited text file containing O2 peaks identified using MACS.

Submission date

May 11, 2018

Last update date

Sep 14, 2018

Contact name

Ramin Yadegari

E-mail(s)

yadegari@email.arizona.edu

Phone

520-621-1616

Organization name

University of Arizona