RNA-seq

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: RNA-seq (NCBI BioProject PRJNA267116)

The objective of this project is to generate transcriptional sequence data from a variety of structures from Malus fusca (Oregon Crab Apple), grown under field conditions or in controlled environment, at multiple time points over the course of one growing season and during development. The data can be linked with ChIP-seq data targeting transcriptionally relevant modifications of histone H3. 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.

Data key:

FastQC file: Raw files were analyzed by FastQC (Version 0.10.1; Babraham Bioinformatics)
SeanQC: Raw files were analyzed for repetitive sequence, sequence not mapping to the Malus genome, and organellar sequence. Potentially problematic datasets are indicated by a yellow or red icon.
Sequence file (1M): File contains 1 million randomly selected sequences from the raw file. Pair-end information was not used.

Sample	Sample code	Stage	Description	Replicate	Reads (M)	Pair-End	FastQC file	SeanQC	Sequence file (Full)	Sequence file (1M)
Flower	1	F1	Flower buds, not including pedicel; sepals enclose remainder of flower bud, ~2 weeks prior to anthesis	1	16.6	R1	Fastqc		Full	1M
				1	16.6	R2	Fastqc		Full	1M
				2	17.1	R1	Fastqc		Full	1M
				2	17.1	R2	Fastqc		Full	1M
				3	9.3	R1	Fastqc		Full	1M
				3	9.3	R2	Fastqc		Full	1M
Pedicel	2	F1	Pedicels from several flowers in a cluster	1	19.5	R1	Fastqc		Full	1M
				1	19.5	R2	Fastqc		Full	1M
				2	14.2	R1	Fastqc		Full	1M
				2	14.2	R2	Fastqc		Full	1M
				3	9.4	R1	Fastqc		Full	1M
				3	9.4	R2	Fastqc		Full	1M
Rachis	3	F1	Stem of inflorescence (rachis) following flower removal not including pedicels	1	21.7	R1	Fastqc		Full	1M
				1	21.7	R2	Fastqc		Full	1M
				2	18.6	R1	Fastqc		Full	1M
				2	18.6	R2	Fastqc		Full	1M
				3	9.3	R1	Fastqc		Full	1M
				3	9.3	R2	Fastqc		Full	1M
Leaf	4	F1	Mostly or fully expanded leaves from several nodes along stem including vegetative nodes near the base and flowering nodes closer to the apex. Includes midvein	1	18.7	R1	Fastqc		Full	1M
				1	18.7	R2	Fastqc		Full	1M
				2	14	R1	Fastqc		Full	1M
				2	14	R2	Fastqc		Full	1M
				3	9.6	R1	Fastqc		Full	1M
				3	9.6	R2	Fastqc		Full	1M
Petiole	5	F1	Petioles from mostly or fully expanded leaves from several nodes along stem including vegetative nodes near the base and flowering nodes closer to the apex	1	11.5	R1	Fastqc		Full	1M
				1	11.5	R2	Fastqc		Full	1M
				3	9.5	R1	Fastqc		Full	1M
				3	9.5	R2	Fastqc		Full	1M
Bark vascular cambium	6	F1	Skin including tissues to 0.5 mm depth from shoot internodes	2	14.2	R1	Fastqc		Full	1M
				2	14.2	R2	Fastqc		Full	1M
				3	10.4	R1	Fastqc		Full	1M
				3	10.4	R2	Fastqc		Full	1M
Shoot apex	8	F1	Terminal apex of new shoots developing from axillary buds on 1-year-old shoots includes leaves <5 mm in length	1	16.2	R1	Fastqc		Full	1M
				1	16.2	R2	Fastqc		Full	1M
				2	14.7	R1	Fastqc		Full	1M
				2	14.7	R2	Fastqc		Full	1M
				3	9	R1	Fastqc		Full	1M
				3	9	R2	Fastqc		Full	1M
Flower	9	F2	Entire flower buds not including pedicels; petals emerging	1	15.3	R1	Fastqc		Full	1M
				1	15.3	R2	Fastqc		Full	1M
				2	17.2	R1	Fastqc		Full	1M
				2	17.2	R2	Fastqc		Full	1M
				3	9.9	R1	Fastqc		Full	1M
				3	9.9	R2	Fastqc		Full	1M
Pedicel	10	F2	Flower pedicels	1	13.2	R1	Fastqc		Full	1M
				1	13.2	R2	Fastqc		Full	1M
				2	14	R1	Fastqc		Full	1M
				2	14	R2	Fastqc		Full	1M
				3	8.8	R1	Fastqc		Full	1M
				3	8.8	R2	Fastqc		Full	1M
Rachis	11	F2	Stem of inflorescence (rachis) following flower removal not including pedicels	1	7.7	R1	Fastqc		Full	1M
				1	7.7	R2	Fastqc		Full	1M
				2	19.5	R1	Fastqc		Full	1M
				2	19.5	R2	Fastqc		Full	1M
				3	9.4	R1	Fastqc		Full	1M
				3	9.4	R2	Fastqc		Full	1M
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	1	14	R1	Fastqc		Full	1M
				1	14	R2	Fastqc		Full	1M
				2	16.5	R1	Fastqc		Full	1M
				2	16.5	R2	Fastqc		Full	1M
				3	9.1	R1	Fastqc		Full	1M
				3	9.1	R2	Fastqc		Full	1M
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	1	11.2	R1	Fastqc		Full	1M
				1	11.2	R2	Fastqc		Full	1M
				2	7.7	R1	Fastqc		Full	1M
				2	7.7	R2	Fastqc		Full	1M
				3	3.2	R1	Fastqc		Full	1M
				3	3.2	R2	Fastqc		Full	1M
Petiole	14	F2	Petioles from mostly or fully expanded leaves from several nodes along stem including vegetative nodes near the base and flowering nodes closer to the apex	1	9.5	R1	Fastqc		Full	1M
				1	9.5	R2	Fastqc		Full	1M
				2	18.8	R1	Fastqc		Full	1M
				2	18.8	R2	Fastqc		Full	1M
				3	9.2	R1	Fastqc		Full	1M
				3	9.2	R2	Fastqc		Full	1M
Petal	15	F2	Flower petals ~1 week prior to anthesis	1	12.3	R1	Fastqc		Full	1M
				1	12.3	R2	Fastqc		Full	1M
				2	9.6	R1	Fastqc		Full	1M
				2	9.6	R2	Fastqc		Full	1M
				3	9.4	R1	Fastqc		Full	1M
				3	9.4	R2	Fastqc		Full	1M
Pistil	16	F2	Flower pistils ~1 week prior to anthesis	1	23.6	R1	Fastqc		Full	1M
				1	23.6	R2	Fastqc		Full	1M
				2	13.5	R1	Fastqc		Full	1M
				2	13.5	R2	Fastqc		Full	1M
				3	7.9	R1	Fastqc		Full	1M
				3	7.9	R2	Fastqc		Full	1M
Receptacle	17	F2	Flower receptacles ~1 week prior to anthesis	1	21	R1	Fastqc		Full	1M
				1	21	R2	Fastqc		Full	1M
				2	8.5	R1	Fastqc		Full	1M
				2	8.5	R2	Fastqc		Full	1M
				3	9	R1	Fastqc		Full	1M
				3	9	R2	Fastqc		Full	1M
Sepal	18	F2	Flower sepals ~1 week prior to anthesis	1	12.2	R1	Fastqc		Full	1M
				1	12.2	R2	Fastqc		Full	1M
				2	9.4	R1	Fastqc		Full	1M
				2	9.4	R2	Fastqc		Full	1M
				3	8.8	R1	Fastqc		Full	1M
				3	8.8	R2	Fastqc		Full	1M
Stamen	19	F2	Flower stamens ~1 week prior to anthesis	1	18.6	R1	Fastqc		Full	1M
				1	18.6	R2	Fastqc		Full	1M
				2	10.1	R1	Fastqc		Full	1M
				2	10.1	R2	Fastqc		Full	1M
				3	8.3	R1	Fastqc		Full	1M
				3	8.3	R2	Fastqc		Full	1M
Bark vascular cambium	20	F2	Skin including tissues to 0.5 mm depth from shoot internodes	3	8.8	R1	Fastqc		Full	1M
Bark vascular cambium	20	F2		3	8.8	R2	Fastqc		Full	1M
Shoot apex	22	F2	Terminal apex of new shoots developing from axillary buds on 1-year-old shoots includes leaves <1 mm in length	1	21.2	R1	Fastqc		Full	1M
				1	21.2	R2	Fastqc		Full	1M
				2	15.7	R1	Fastqc		Full	1M
				2	15.7	R2	Fastqc		Full	1M
				3	8.3	R1	Fastqc		Full	1M
				3	8.3	R2	Fastqc		Full	1M
Anther	23	F3	Anthers at anthesis	2	18.3	R1	Fastqc		Full	1M
				2	18.3	R2	Fastqc		Full	1M
				3	8.8	R1	Fastqc		Full	1M
				3	8.8		Fastqc		Full	1M
Shoot apex	24	F3	Terminal apex of new shoots developing from axillary buds on 1-year-old shoots includes leaves <1 mm in length	1	13.1	R1	Fastqc		Full	1M
				1	13.1	R2	Fastqc		Full	1M
				3	8.7	R1	Fastqc		Full	1M
				3	8.7	R2	Fastqc		Full	1M
Filament	25	F3	Stamen filaments at anthesis	1	16.9	R1	Fastqc		Full	1M
				1	16.9	R2	Fastqc		Full	1M
				3	8.2	R1	Fastqc		Full	1M
				3	8.2	R2	Fastqc		Full	1M
Ovary	26	F3	Basal section of pistils at anthesis	1	14.2	R1	Fastqc		Full	1M
				1	14.2	R2	Fastqc		Full	1M
				2	23.5	R1	Fastqc		Full	1M
				2	23.5	R2	Fastqc		Full	1M
				3	9.9	R1	Fastqc		Full	1M
				3	9.9	R2	Fastqc		Full	1M
Petal	27	F3	Flower petals at anthesis	2	12.6	R1	Fastqc		Full	1M
				2	12.6	R2	Fastqc		Full	1M
				3	8.2	R1	Fastqc		Full	1M
				3	8.2	R2	Fastqc		Full	1M
Pollen	28	F3	Pollen at anthesis	2	11.5	R1	Fastqc		Full	1M
				2	11.5	R2	Fastqc		Full	1M
				3	9.2	R1	Fastqc		Full	1M
				3	9.2	R2	Fastqc		Full	1M
Trichome	29	F3	Trichomes from petiols and pedicels	1	15.1	R1	Fastqc		Full	1M
Trichome	29	F3	Trichomes from petiols and pedicels	1	15.1	R2	Fastqc		Full	1M
Sepal	30	F3	Flower sepals at anthesis	3	8.3	R1	Fastqc		Full	1M
Sepal	30	F3	Flower sepals at anthesis	3	8.3	R2	Fastqc		Full	1M
Stigma	31	F3	Stigmas from flowers at anthesis	1	12.5	R1	Fastqc		Full	1M
				1	12.5	R2	Fastqc		Full	1M
				3	7	R1	Fastqc		Full	1M
				3	7	R2	Fastqc		Full	1M
Style	32	F3	Styles from flowers at anthesis	3	8.4	R1	Fastqc		Full	1M
Style	32	F3	Styles from flowers at anthesis	3	8.4	R2	Fastqc		Full	1M
Leaf	33	F3	Leaves 1-5 mm from terminal apices of new shoots	1	18.2	R1	Fastqc		Full	1M
				1	18.2	R2	Fastqc		Full	1M
				3	9.4	R1	Fastqc		Full	1M
				3	9.4	R2	Fastqc		Full	1M
Shoot apex	34	F4	Terminal apex and axillary buds of new shoots includes leaves <1 mm in length	1	11.9	R1	Fastqc		Full	1M
				1	11.9	R2	Fastqc		Full	1M
				3	9.5	R1	Fastqc		Full	1M
				3	9.5	R2	Fastqc		Full	1M
Fruit minus seeds	35	F4	Fruit minus seeds ~1 week after anthesis	1	9.6	R1	Fastqc		Full	1M
				1	9.6	R2	Fastqc		Full	1M
				3	9.7	R1	Fastqc		Full	1M
				3	9.7	R2	Fastqc		Full	1M
Seed	36	F4	Fertilized ovules ~1 week after anthesis	3	13	R1	Fastqc		Full	1M
Seed	36	F4	Fertilized ovules ~1 week after anthesis	3	13	R2	Fastqc		Full	1M
Leaf	37	F4	Leaves 1-5 mm from terminal apices of new shoots	1	15.6	R1	Fastqc		Full	1M
				1	15.6	R2	Fastqc		Full	1M
				3	8.9	R1	Fastqc		Full	1M
				3	8.9	R2	Fastqc		Full	1M
Shoot apex	38	F5	Terminal apex and axillary buds of new shoots includes leaves <1 mm in length	3	8.4	R1	Fastqc		Full	1M
Shoot apex	38	F5		3	8.4	R2	Fastqc		Full	1M
Embryo	39	F5	Embryo dissected from seed 1 mm or less in diameter ~3 weeks after anthesis	3	9.1	R1	Fastqc		Full	1M
Embryo	39	F5		3	9.1	R2	Fastqc		Full	1M
Fruit minus seeds	40	F5	Fruit minus seeds ~3 weeks after anthesis	3	7.7	R1	Fastqc		Full	1M
Fruit minus seeds	40	F5	Fruit minus seeds ~3 weeks after anthesis	3	7.7	R2	Fastqc		Full	1M
Leaf	41	F5	Blade from more basal leaf of new shoot ~8 weeks after emergence	3	8.3	R1	Fastqc		Full	1M
Leaf	41	F5		3	8.3	R2	Fastqc		Full	1M
Seed	42	F5	Immature seeds ~three weeks after anthesis	3	8.4	R1	Fastqc		Full	1M
Seed	42	F5	Immature seeds ~three weeks after anthesis	3	8.4	R2	Fastqc		Full	1M
Leaf	44	F5	Blade from more apical leaf of new shoot ~1 week after emergence	1	9.6	R1	Fastqc		Full	1M
				1	9.6	R2	Fastqc		Full	1M
				2	11	R1	Fastqc		Full	1M
				2	11	R2	Fastqc		Full	1M
Embryo	48	F6	Embryo ~6 weeks after anthesis	1	13.2	R1	Fastqc		Full	1M
				1	13.2	R2	Fastqc		Full	1M
				3	7.9	R1	Fastqc		Full	1M
				3	7.9	R2	Fastqc		Full	1M
Fruit minus seeds	49	F6	Fruit minus seeds ~6 weeks after anthesis	3	8.5	R1	Fastqc		Full	1M
Fruit minus seeds	49	F6	Fruit minus seeds ~6 weeks after anthesis	3	8.5	R2	Fastqc		Full	1M
Seed coat	51	F6	Seed coat including some endosperm ~6 weeks after anthesis	3	7.6	R1	Fastqc		Full	1M
Seed coat	51	F6	Seed coat including some endosperm ~6 weeks after anthesis	3	7.6	R2	Fastqc		Full	1M
Shoot apex	52	F7	Terminal and axillary buds of new shoots includes leaves <1 mm in length	3	8.8	R1	Fastqc		Full	1M
Shoot apex	52	F7		3	8.8	R2	Fastqc		Full	1M
Embryo	53	F7	Embryo ~9 weeks after anthesis	3	8	R1	Fastqc		Full	1M
Embryo	53	F7	Embryo ~9 weeks after anthesis	3	8	R2	Fastqc		Full	1M
Fruit minus seeds	54	F7	Fruit minus seeds ~9 weeks after anthesis	3	8.2	R1	Fastqc		Full	1M
Fruit minus seeds	54	F7	Fruit minus seeds ~9 weeks after anthesis	3	8.2	R2	Fastqc		Full	1M
Seed coat	55	F7	Seed coat ~9 weeks after anthesis	3	8.3	R1	Fastqc		Full	1M
Seed coat	55	F7	Seed coat ~9 weeks after anthesis	3	8.3	R2	Fastqc		Full	1M
Shoot apex	56	F8	Terminal and axillary buds of new shoots includes leaves <1 mm in length	3	9.1	R1	Fastqc		Full	1M
Shoot apex	56	F8		3	9.1	R2	Fastqc		Full	1M
Embryo	57	F8	Embryo ~13 weeks after anthesis	3	8.8	R1	Fastqc		Full	1M
Embryo	57	F8	Embryo ~13 weeks after anthesis	3	8.8	R2	Fastqc		Full	1M
Fruit minus seeds	58	F8	Fruit minus seeds ~13 weeks after anthesis	3	7.2	R1	Fastqc		Full	1M
Fruit minus seeds	58	F8	Fruit minus seeds ~13 weeks after anthesis	3	7.2	R2	Fastqc		Full	1M
Seed coat	59	F8	Seed coat ~13 weeks after anthesis	3	7.6	R1	Fastqc		Full	1M
Seed coat	59	F8	Seed coat ~13 weeks after anthesis	3	7.6	R2	Fastqc		Full	1M
Shoot apex	60	F9	Terminal and axillary buds of new shoots includes leaves <1 mm in length	3	6.6	R1	Fastqc		Full	1M
Shoot apex	60	F9		3	6.6	R2	Fastqc		Full	1M
Embryo	62	F9	Embryo ~16 weeks after anthesis	3	4.4	R1	Fastqc		Full	1M
Embryo	62	F9	Embryo ~16 weeks after anthesis	3	4.4	R2	Fastqc		Full	1M
Fruit minus seeds and skin	63	F9	Fruit minus seeds and skin ~16 weeks after anthesis	3	7.5	R1	Fastqc		Full	1M
Fruit minus seeds and skin	63	F9	Fruit minus seeds and skin ~16 weeks after anthesis	3	7.5	R2	Fastqc		Full	1M
Seed coat	64	F9	Seed coat ~16 weeks after anthesis	3	8.1	R1	Fastqc		Full	1M
Seed coat	64	F9	Seed coat ~16 weeks after anthesis	3	8.1	R2	Fastqc		Full	1M
Fruit skin	65	F9	Fruit skin green ~13 weeks after anthesis	3	7.4	R1	Fastqc		Full	1M
Fruit skin	65	F9	Fruit skin green ~13 weeks after anthesis	3	7.4	R2	Fastqc		Full	1M
Fruit skin	66	F9	Fruit skin purple ~13 weeks after anthesis	3	8.1	R1	Fastqc		Full	1M
Fruit skin	66	F9	Fruit skin purple ~13 weeks after anthesis	3	8.1	R2	Fastqc		Full	1M
Shoot apex	67	F10	Terminal and axillary buds of new shoots includes leaves <1 mm in length	3	7.2	R1	Fastqc		Full	1M
Shoot apex	67	F10		3	7.2	R2	Fastqc		Full	1M
Embryo	68	F10	Embryo beginning to harden ~19 weeks after anthesis	3	7.6	R1	Fastqc		Full	1M
Embryo	68	F10	Embryo beginning to harden ~19 weeks after anthesis	3	7.6	R2	Fastqc		Full	1M
Fruit minus seeds and skin	69	F10	Fruit minus seeds and skin ~19 weeks after anthesis	3	6.1	R1	Fastqc		Full	1M
Fruit minus seeds and skin	69	F10	Fruit minus seeds and skin ~19 weeks after anthesis	3	6.1	R2	Fastqc		Full	1M
Shoot apex	70	LB2	Shoot apices of 14-week-old seedlings includes leaves <1 mm in length	2	8.5	R1	Fastqc		Full	1M
Shoot apex	70	LB2		2	8.5	R2	Fastqc		Full	1M
Shoot apex	72	LB3	Shoot apices of 26-week-old seedlings includes leaves <1 mm in length	2	7.7	R1	Fastqc		Full	1M
Shoot apex	72	LB3		2	7.7	R2	Fastqc		Full	1M
Leaf	73	LB2	Apical leaves from 14-week-old plants	1	4.8	R1	Fastqc		Full	1M
				1	4.8	R2	Fastqc		Full	1M
				2	5.1	R1	Fastqc		Full	1M
				2	5.1	R2	Fastqc		Full	1M
Leaf	74	LB1	Apical leaves from 2-week-old plants	1	5.5	R1	Fastqc		Full	1M
				1	5.5	R2	Fastqc		Full	1M
				2	7.5	R1	Fastqc		Full	1M
				2	7.5	R2	Fastqc		Full	1M
Shoot apex	76	LA1	Terminal shoot apex of three-week-old seedlings from growth chamber	2	13.1	R1	Fastqc		Full	1M
				2	13.1	R2	Fastqc		Full	1M
				3	7.5	R1	Fastqc		Full	1M
				3	7.5	R2	Fastqc		Full	1M
Cotyledon	77	LA1	Cotyledons from three-week-old seedlings predominately green	1	14.5	R1	Fastqc		Full	1M
				1	14.5	R2	Fastqc		Full	1M
				2	18.6	R1	Fastqc		Full	1M
				2	18.6	R2	Fastqc		Full	1M
				3	7.3	R1	Fastqc		Full	1M
				3	7.3	R2	Fastqc		Full	1M
Leaf	78	LA1	Leaves 1 to 5 mm in length from apex of three-week-old seedlings	1	15.5	R1	Fastqc		Full	1M
				1	15.5	R2	Fastqc		Full	1M
				2	16.5	R1	Fastqc		Full	1M
				2	16.5	R2	Fastqc		Full	1M
				3	7.7	R1	Fastqc		Full	1M
				3	7.7	R2	Fastqc		Full	1M
Hypocotyl	79	LA1	Hypocotyls of three-week-old seedlings	1	14.4	R1	Fastqc		Full	1M
				1	14.4	R2	Fastqc		Full	1M
				3	7.6	R1	Fastqc		Full	1M
				3	7.6	R2	Fastqc		Full	1M
Root	80	LA1	All roots from three-week-old seedlings	3	7.6	R1	Fastqc		Full	1M
Root	80	LA1	All roots from three-week-old seedlings	3	7.6	R2	Fastqc		Full	1M
Stem petiole	81	LA1	Main stem above cotyledon and petioles of three-week-old seedlings	3	7.8	R1	Fastqc		Full	1M
Stem petiole	81	LA1		3	7.8	R2	Fastqc		Full	1M
Leaf	82	LA1	Blade of mostly or fully expanded leaves from three-week-old seedlings	1	15.2	R1	Fastqc		Full	1M
				1	15.2	R2	Fastqc		Full	1M
				2	24.8	R1	Fastqc		Full	1M
				2	24.8	R2	Fastqc		Full	1M
				3	7.5	R1	Fastqc		Full	1M
				3	7.5	R2	Fastqc		Full	1M

Sample

Sample code

Stage

Description

Replicate

Reads (M)

Pair-End

FastQC file

SeanQC

Sequence file (Full)

Sequence file (1M)

Flower

1

F1

Flower buds, not including pedicel; sepals enclose remainder of flower bud, ~2 weeks prior to anthesis

1

16.6

R1

R2

2

17.1

R1

R2

3

9.3

R1

R2

Pedicel

2

F1

Pedicels from several flowers in a cluster

1

19.5

R1

R2

2

14.2

R1

R2

3

9.4

R1

R2

Rachis

3

F1

Stem of inflorescence (rachis) following flower removal not including pedicels

1

21.7

R1

R2

2

18.6

R1

R2

3

9.3

R1

R2

Leaf

4

F1

Mostly or fully expanded leaves from several nodes along stem including vegetative nodes near the base and flowering nodes closer to the apex. Includes midvein

1

18.7

R1

R2

2