National Science Foundation
Division of Biological Infrastructure
Plant Genome Research Program

Exploiting Chromatin Landmarks to Characterize Complex Plant Genomes

Project DBI-0922447
Steve van Nocker, PI vannocke@msu.edu

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Data Access and Annotation: Chromatin-tagged sequence (CTS)

Malus domestica epigenomics

NCBI BioProject PRJNA267727

The objective of this project is to generate ChIP-seq (chromatin immunoprecipitate sequence) data from shoot apex and leaf from Malus x domestica, grown under field conditions. This efforts targets histone H3 post-translational modifications H3K4me3, H3K36me2, and H3K27me3, as well as total H3. The data can be linked with transcriptional data generated from the same samples. Results may be used to facilitate sequence analysis of gene-rich regions in plants with complex genomes, identify chromatin landmarks useful for genome annotation, and identify polymorphic sequences most useful for genetic map construction. The project is expected to help uncover how chromatin structure is linked to gene activity, add accuracy to annotation efforts, and uncover cryptic and previously unanticipated features of plant genomes.

Sequences posted here were filtered using Fastq-mcf to remove poor quality reads, poor quality bases and adapters, followed by a custom Python script to remove A/T rich sequences and sequence regions, as well as filtered sequences less than 19 b in length.

Sample	Description	Replicate	Target	Reads (M)	Sequence File(s) (GB)
Leaf	Leaf from field-grown Malus domestica, cv. Golden Delicious, partially or fully expanded apical leaf; new shoot has 6-10 visible leaves. NCBI Biosample SAMN03199814		Input	225.9	LF-Chr.fastq.mcf.san.gz (19.1)
		1	H3-CT	26.6	LF-B1-CT.fastq.mcf.san.gz (2.3)
			H3K4me3	12.3	LF-B1-K4.fastq.mcf.san.gz (1.0)
			H3K27me3	16.1	LF-B1-K27.fastq.mcf.san.gz (1.3)
			H3K36me2	8.7	LF-B1-K36.fastq.mcf.san.gz (0.7)
		2	H3-CT	23.2	LF-B2-CT.fastq.mcf.san.gz (2.0)
			H3K4me3	16.8	LF-B2-K4.fastq.mcf.san.gz (1.4)
			H3K27me3	13.3	LF-B2-K27.fastq.mcf.san.gz (1.1)
			H3K36me2	6.0	LF-B2-K36.fastq.mcf.san.gz (0.5)
		3	H3-CT	35.0	LF-B3-T2-CT.fastq.mcf.san.gz (3.0)
			H3K4me3	29.6	LF-B3-T2-K4.fastq.mcf.san.gz (2.5)
			H3K27me3	19.6	LF-B3-T2-K27.fastq.mcf.san.gz (1.6)
			H3K36me2	14.1	LF-B3-T2-K36.fastq.mcf.san.gz (1.2)
Shoot apex	Shoot apex from field-grown Malus domestica, cv. Golden Delicious, new shoot has 6-10 visible leaves. NCBI Biosample SAMN03199813		Input	293.3	AP-Chr.fastq.mcf.san.gz (23.8)
		1	H3-CT	16.9	AP-B1-T2-CT.fastq.mcf.san.gz (1.4)
			H3K4me3	12.2	AP-B1-T2-K4.fastq.mcf.san.gz (1.0)
			H3K27me3	17.6	AP-B1-T2-K27.fastq.mcf.san.gz (1.4)
			H3K36me2	13.5	AP-B1-T2-K36.fastq.mcf.san.gz (1.1)
		2	H3-CT	27.9	AP-B2-CT.fastq.mcf.san.gz (2.3)
			H3K4me3	23.2	AP-B2-K4.fastq.mcf.san.gz (1.9)
			H3K27me3	18.1	AP-B2-K27.fastq.mcf.san.gz (1.5)
			H3K36me2	17.4	AP-B2-K36.fastq.mcf.san.gz (1.4)
		3	Input	22.9	AP-B3-T2-CT.fastq.mcf.san.gz (1.9)
			H3K4me3	33.9	AP-B3-T2-K4.fastq.mcf.san.gz (2.8)
			H3K27me3	28.4	AP-B3-T2-K27.fastq.mcf.san.gz (2.3)
			H3K36me2	19.0	AP-B3-T2-K36.fastq.mcf.san.gz (1.6)

MD5 Checksum file