Data from: Insights into the maize pan-genome and pan-transcriptome

 

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Title Fragments per kilo base of exon model perl million fragments mapped (FPKM) values for 503 diverse maize inbred lines.
Downloaded 184 times
Description This file is a tab delimited file with a header line. The columns in the file are gene name, chromosome, gene start, and gene stop followed by the expression data for the 503 inbred lines.
Download maize_503genotypes_raw_expression_values_FPKM.txt (152.1 Mb)
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Title Single Nucleotide Polymorphisms (SNPs) for 503 diverse maize inbred lines.
Downloaded 431 times
Description This is a tab delimited file with a header line that contains raw SNP data for 485,179 SNPs across 503 diverse maize inbred lines. The file contains a column for chromosome, position, the reference B73 v2 allele, number of missing data points, and observed alleles across the 503 inbred lines, followed by the data for the 503 inbred lines.
Download maize_503genotypes_485179SNPs_working_SNP_set.txt (499.4 Mb)
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Title Transcript assemblies for representative transcripts generated in individual assemblies for 366 diverse maize inbred lines.
Downloaded 77 times
Description The assemblies were generated from reads that could not be mapped to the maize v2 reference sequence. Only the representative transcript assembly for each locus, defined as the longest transcript within the locus, is presented in the file.
Download individual_assembly_747977_RTAs.fasta (383.7 Mb)
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Title Transcript assemblies for representative transcripts generated in a joint assembly across 503 diverse maize inbred lines.
Downloaded 82 times
Description The assembly was generated from reads that could not be mapped to the maize v2 reference sequence. Only the representative transcript assembly for each locus, defined as the longest transcript within the locus, is presented in the file.
Download joint_assembly_8681_RTAs.fasta (8.369 Mb)
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Title Genome wide association study (GWAS) results for growing degree days to pollen shed, growing degree days to silk, and last leaf with juvenile wax.
Downloaded 4687 times
Description The file is a tab delimated file with a header that contains GWAS results presented as p-values for ~438K SNPs. The columns in the file are SNP, chromosome, position, growing degree days to pollen shed p- values, growing degree days to silk p-values, and last leaf with juvenile wax p-values.
Download 438K_Imputed_GWASresults_withRTA.txt (35.93 Mb)
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Title Imputed Genotype Scores 438K Single Nucleotide Polymorphisms across 503 diverse maize inbred lines
Downloaded 602 times
Description The file is a CSV file with a header that contains genotype scores imputed using GAPIT.
Download GAPIT.RNAseq.hmp_438K_imputed2.csv (1.123 Gb)
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When using this data, please cite the original publication:

Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Peñagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR (2014) Insights into the maize pan-genome and pan-transcriptome. The Plant Cell 26(1): 121-135. http://dx.doi.org/10.1105/tpc.113.119982

Additionally, please cite the Dryad data package:

Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Peñagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR (2014) Data from: Insights into the maize pan-genome and pan-transcriptome. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r73c5
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