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Sample GSM4886813

Query DataSets for GSM4886813

Status

Public on Apr 26, 2021

Title

Soybean_input

Sample type

SRA

Source name

leaf

Organism

Glycine max

Characteristics

tissue: leaf
strain: William82
chip antibody: none (input)

Treatment protocol

No Treatmant

Growth protocol

Glycine max (accession William82) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). The 2nd and 3rd leaves were collected for the experiments. For Zea mays Ear primordia protocol: Plants were grown in greenhouse or field conditions. Plants were harvested approximately one month after sowing and ear primordia were dissected from shoots. Ear primordia were harvested from any node of the shoot if they were within the desired size range: between 3 to 8 millimeters from the base to the apical tip of the ear.

Extracted molecule

genomic DNA

Extraction protocol

ChiP-seq was performed following the methods of (Zang et al. 2007). Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation
Antibidies Used: Anti-trimethyl-Histone H3 (Lys4) [EMD Millipore, Cat#:07-473], Anti-Histone H3 (tri methyl K36) [Abcam, Cat#:ab9050], Anti-acetyl-Histone H3 (Lys56) [EMD Millipore, Cat#:07-677-I]

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NovaSeq 6000

Description

input

Data processing

Reads were trimmed using trimmomatic, and aligned to the genome using bowtie2, `--very-sensitive`. Only uniquely mapping reads were used for downstream analysism, with duplicates being removed using the picard MarkDuplicates command.
Peak calling was done for histone modifications known to have broad peaks (H3K36me3, and H3K4me1) using the software epic2 with the parameters “--false-discovery-rate-cutoff .1 --keep-duplicates”, as well as MACS2 to identify smaller regions of enrichment using the parameters `callpeak --keep-dup all -g 1.6e9 -q .1`. Narrow peaks (H3K56ac and H3K4me3) were called using MACS2 with the parameters “ --keep-dup all --extsize 147 -g 1.6e9 -p .05’ (Stovner and Sætrom, 2019, p. 2; Zhang et al., 2008). Peaks which were within 480 bps, or roughly two nucleosomes of each other were merged. Intersection between replicates of the same histone modification were taken, and the total length of the two overlapping segments were taken.
Genome_build: Z. mays genome and gene annotation AGPv4
Supplementary_files_format_and_content: bed files. Column1: Chromosome; Column2: Start of Peak; Column3: End of peak

Submission date

Nov 05, 2020

Last update date

Apr 26, 2021

Contact name

Robert J Schmitz

E-mail(s)

[email protected]

Organization name

University of Georgia

Department

Genetics