Browsing by Author "University of Minnesota Springer Lab"

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    Data for: Meta gene regulatory networks in maize highlight functionally relevant regulatory interactions
    (2020-03-12) Zhou, Peng; Springer, Nathan M.; zhoux379@umn.edu; Zhou, Peng; University of Minnesota Springer Lab
    Regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent a map of potential transcriptional regulation. A consistent analysis of a large number of public maize transcriptome datasets including >6000 RNA-Seq samples was used to generate 45 co- expression based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, tissue-and-genotype, etc). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes.
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    Maize Mo17 SNPs
    (2018-07-11) Zhou, Peng; zhoux379@umn.edu; Zhou, Peng; University of Minnesota Springer Lab
    Genome resequencing of Mo17 was done as part of the bioMAP project (REF). 477 million 100bp paired-end reads were generated for Mo17 giving an average of 95x coverage. Reads were first trimmed by Trimmomatic (Bolger et al. 2014) and mapped to the maize B73 genome AGPv4 (Jiao et al. 2017) using BWA-MEM (Li and Durbin 2010). PCR duplicates were marked and removed using GATK (McKenna et al. 2010). Variants were called by GATK haplotypecaller and filtered using different filters for SNPs: (QD > 2, FS < 60, MQ > 40, MQRankSum > -12.5, ReadPosRankSum > -8, SOR < 4) and for InDels: (QD > 2, FS < 200, ReadPosRankSum > -20, SOR < 10). Moreover, variants located in regions with unusually high coverage (DP > Mean + 2*SD) and heterozygous calls (GT == '0/1') were also removed. The final variant file containing 8.04 million variants with 164 thousand CDS variants was deposited in DRUM.