Chromatin-tagged sequence

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

Data Access and Annotation: Chromatin-tagged sequence (CTS) (Malus fusca) NCBI BioProject PRJNA267588

The objective of this project is to generate ChIP-seq (chromatin immunoprecipitate sequence) data from a variety of structures from Malus fusca (Oregon Crab Apple), grown under field conditions or controlled environment, at multiple time points over the course of one growing season and during development. 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

Sample	Sample Code	Stage	Description	Target	Sequence File(s)
Flower	1	F1	Flower buds, not including pedicel; sepals enclose remainder of flower bud, ~2 weeks prior to anthesis	H3-CT	C1_CT.fastq.gz
				H3K4me3	C1_K4.fastq.gz
				H3K27me3	C1_K27.fastq.gz
				H3K36me2	C1_K36.fastq.gz
Flower	9	F2	Entire flower buds not including pedicels; petals emerging	H3-CT	C9_CT_1.fastq.gz C9_CT_2.fastq.gz
				H3K4me3	C9_K4_1.fastq.gz C9_K4_2.fastq.gz
				H3K27me3	C9_K27_1.fastq.gz C9_K27_2.fastq.gz
				H3K36me2	C9_K36_1.fastq.gz C9_K36_2.fastq.gz
Leaf	12	F2	Mostly or fully expanded leaves from several nodes along stem including vegetative nodes near the base and flowering nodes closer to the apex	H3-CT	C12_CT.fastq.gz
				H3K27me3	C12_K27.fastq.gz
				H3K36me2	C12_K36.fastq.gz
Leaf midvein	13	F2	Midveins from mostly or fully expanded leaves from several nodes along stem including vegetative nodes near the base and flowering nodes closer to the apex	H3CT	C13_CT.fastq.gz
				H3K4me3	C13_K4.fastq.gz
				H3K27me3	C13_K27.fastq.gz
Receptacle	17	F2	Flower receptacles ~1 week prior to anthesis	H3CT	C17_CT.fastq.gz
				H3K27me3	C17_K27.fastq.gz
				H3K36me2	C17_K36.fastq.gz
Stamen	19	F2	Flower stamens ~1 week prior to anthesis	H3CT	C19_CT.fastq.gz
				H3K4me3	C19_K4.fastq.gz
				H3K27me3	C19_K27.fastq.gz
				H3K36me2	C19_K36.fastq.gz
Bark vascular cambium	20	F2	Skin including tissues to 0.5 mm depth from shoot internodes	H3CT	C20_CT.fastq.gz
				H3K27me3	C20_K27.fastq.gz
				H3K36me2	C20_K36.fastq.gz
Shoot apex	22	F2	Terminal apex of new shoots developing from axillary buds on 1-year-old shoots includes leaves <1 mm in length	H3CT	C22_CT.fastq.gz
Shoot apex	22	F2		H3K36me2	C22_K36.fastq.gz
Filament	25	F3	Stamen filaments at anthesis	H3CT	C25_CT.fastq.gz
				H3K27me3	C25_K27.fastq.gz
				H3K36me2	C25_K36.fastq.gz
Petal	27	F3	Flower petals at anthesis	H3CT	C27_CT.fastq.gz
				H3K4me3	C27_K4.fastq.gz
				H3K27me3	C27_K27.fastq.gz
				H3K36me2	C27_K36.fastq.gz
Style	32	F3	Styles from flowers at anthesis	H3CT	C32_CT.fastq.gz
Style	32	F3	Styles from flowers at anthesis	H3K36me2	C32_K36.fastq.gz
Shoot apex	52	F7	Terminal and axillary buds of new shoots includes leaves <1 mm in length	H3CT	C52_CT.fastq.gz
				H3K4me3	C52_K4.fastq.gz
				H3K27me3	C52_K27.fastq.gz
				H3K36me2	C52_K36.fastq.gz
Embryo	68	F10	Embryo beginning to harden ~19 weeks after anthesis	H3CT	C68_CT.fastq.gz
				H3K4me3	C68_K4.fastq.gz
				H3K27me3	C68_K27.fastq.gz
				H3K36me2	C68_K36.fastq.gz
Shoot apex	76	LA1	Terminal shoot apex of three-week-old seedlings from growth chamber	H3CT	C76_CT.fastq.gz
				H3K4me3	C76_K4.fastq.gz
				H3K27me3	C76_K27.fastq.gz
Leaf	78	LA1	Leaves 1 to 5 mm in length from apex of three-week-old seedlings	H3CT	C78_CT.fastq.gz
				H3K27me3	C78_K27.fastq.gz
				H3K36me2	C78_K36.fastq.gz
Hypocotyl	79	LA1	Hypocotyls of three-week-old seedlings	H3CT	C79_CT.fastq.gz
				H3K4me3	C79_K4.fastq.gz
				H3K36me2	C79_K36.fastq.gz
Leaf	82	LA1	Blade of mostly or fully expanded leaves from three-week-old seedlings	H3CT	C82_CT.fastq.gz
				H3K4me3	C82_K4.fastq.gz
				H3K27me3	C82_K27.fastq.gz
				H3K36me2	C82_K36.fastq.gz