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Series GSE136685 Query DataSets for GSE136685
Status Public on Jun 05, 2020
Title The regulatory landscape of early maize inflorescence development
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements and regulatory DNA revealed through chromatin accessibility maps can be harnessed for manipulating gene expression to subtle phenotypic outputs that enhance productivity in specific environments. Here, we present a genome-wide view of accessible chromatin and nucleosome occupancy at a very early stage in the development of both pollen- and grain-bearing inflorescences of the important cereal crop maize (Zea mays), using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion. Results showed that in these largely undifferentiated tissues, approximately 1.5-4 percent of the genome is accessible, with the majority of MNase hypersensitive sites marking proximal promoters but also 3’ flanks of maize genes. This approach mapped regulatory elements to footprint-level resolution, and through integration of complementary transcriptome and transcription factor occupancy data, we annotated regulatory factors such as combinatorial motifs and long non-coding RNAs that potentially contribute to organogenesis in maize inflorescence development, including tissue-specific regulation between male and female structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity, revealed new SNP-trait associations in known regulators of inflorescence development. These analyses provide a first look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.
 
Overall design As detailed below, we analyzed 2 different tissue types, maize tassel and ear primordia. Nucleosome bound DNA from these primordia were digested with low (light digest) and high (heavy digest) concentration of micrococcal nuclease enzyme followed by high-throughput sequencing to investigate the chromatin landscape. The differential between light and heavy digests and the different size classes of sequenced reads were used to call nucleosomal and transcription factor footprints. Two biological replicates were used per tissue per micrococcal nuclease enzyme concentration.
 
Contributor(s) Parvathaneni RK, Bertolini E, Shamimuzzaman M, Vera D, Lung P, Rice BR, Zhang J, Brown PJ, Lipka AE, Bass HW, Eveland AL
Citation(s) 32631399
Submission date Aug 30, 2019
Last update date Jul 13, 2020
Contact name Andrea Eveland
E-mail(s) AEveland@danforthcenter.org
Organization name Donald Danforth Plant Science Center
Lab Andrea L. Eveland
Street address 975 North Warson Road
City St. Louis
State/province Missouri
ZIP/Postal code 63132
Country USA
 
Platforms (1)
GPL17628 Illumina HiSeq 2500 (Zea mays)
Samples (8)
GSM4055227 Ear_MNase_seq_rep1_light_digest
GSM4055228 Ear_MNase_seq_rep1_heavy_digest
GSM4055229 Ear_MNase_seq_rep2_light_digest
Relations
BioProject PRJNA563086
SRA SRP219942

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136685_AdditionalFile11_DatasetS10.txt.gz 6.6 Mb (ftp)(http) TXT
GSE136685_AdditionalFile16_DatasetS15.zip.gz 82.7 Kb (ftp)(http) ZIP
GSE136685_AdditionalFile2_DatasetS1.txt.gz 100.1 Mb (ftp)(http) TXT
GSE136685_AdditionalFile3_DatasetS2.txt.gz 49.5 Mb (ftp)(http) TXT
GSE136685_AdditionalFile4_DatasetS3.txt.gz 105.5 Mb (ftp)(http) TXT
GSE136685_AdditionalFile5_DatasetS4.txt.gz 72.2 Mb (ftp)(http) TXT
GSE136685_AdditionalFile6_DatasetS5.txt.gz 2.4 Mb (ftp)(http) TXT
GSE136685_Ear_DNS_combo_iSeg_bc_2.0.bed.gz 4.4 Mb (ftp)(http) BED
GSE136685_Ear_DNS_combo_iSeg_bc_3.0.bed.gz 2.8 Mb (ftp)(http) BED
GSE136685_Ear_MNaseheavydigest_combo.bw 1.7 Gb (ftp)(http) BW
GSE136685_Ear_MNaselightdigest_combo.bw 1.7 Gb (ftp)(http) BW
GSE136685_Ear_footprints_iSeg_bc4.0.bed.gz 1.4 Mb (ftp)(http) BED
GSE136685_Ear_light_small_combo_iSeg_bc_2.0.bed.gz 7.4 Mb (ftp)(http) BED
GSE136685_Ear_light_small_combo_iSeg_bc_3.0.bed.gz 3.2 Mb (ftp)(http) BED
GSE136685_RAW.tar 8.3 Gb (http)(custom) TAR (of BED, BW)
GSE136685_Tassel_DNS_combo_iSeg_bc_2.0.bed.gz 5.1 Mb (ftp)(http) BED
GSE136685_Tassel_DNS_combo_iSeg_bc_3.0.bed.gz 3.1 Mb (ftp)(http) BED
GSE136685_Tassel_MNaseheavydigest_combo.bw 1.9 Gb (ftp)(http) BW
GSE136685_Tassel_MNaselightdigest_combo.bw 1.7 Gb (ftp)(http) BW
GSE136685_Tassel_footprints_iSeg_bc4.0.bed.gz 4.5 Mb (ftp)(http) BED
GSE136685_Tassel_light_small_combo_iSeg_bc_2.0.bed.gz 10.1 Mb (ftp)(http) BED
GSE136685_Tassel_light_small_combo_iSeg_bc_3.0.bed.gz 5.4 Mb (ftp)(http) BED
GSE136685_readme_processed_files_descriptions.txt 5.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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