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

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












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
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
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


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