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 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)
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)
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)
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)
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)
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)
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