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Series GSE165787 Query DataSets for GSE165787
Status Public on Feb 01, 2021
Title De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression. 
 
Overall design Genotype pooling of NAM founder leaf tissues across three biological replicates and two technical replicates of single-cell ATAC-seq libraries. Individual cells were genotyped and reads from cells from the same founder were aggregated.
 
Contributor(s) Marand A, Schmitz B
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Submission date Jan 29, 2021
Last update date Apr 27, 2021
Contact name Robert J Schmitz
E-mail(s) schmitz@uga.edu
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platforms (1)
GPL25410 Illumina NovaSeq 6000 (Zea mays)
Samples (104)
GSM5266693 B73.rep1
GSM5266694 B73.rep2
GSM5266695 B73.rep3
Relations
BioProject PRJNA697943
SRA SRP303852

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
GSE165787_NAM_lines_concatenated.ATAC.narrowpeak.gz 48.7 Mb (ftp)(http) NARROWPEAK
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Raw data are available in SRA
Processed data are available on Series record

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