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37 research data, page 1 of 4

Technical validation experiment for reproducibility of high throughput plant phenotyping using LemnaTec automated image acquisition and IAP image analysis workflow

Astrid Junker, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
This dataset describes and quantifies the repeatability of the phenotyping workflow for the LemnaTec facility. Three single Arabidopsis thaliana plants in different developmental stages haven been subjected to repeated imaging over 50 rounds. The evaluation of geometric features extracted from the images using IAP and statistical post-processing revealed a high stability and reproducibility of the established imaging and analysis procedures.

A Preliminary Review of Allium subg. Melanocrommyum in Central Asia

Reinhard M. Fritsch, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
The review (288 pages A4) contains a taxonomic treatment of subg. Melanocrommyum (82 species and subspecies with about 40 synonyms, but no new taxa) affiliated to 17 sections and 21 subsections. Included is also subg. Porphyroprason (1 species, 2 synonyms). The publication starts with a Foreword, a General Introduction into the biological features of subg. Melanocrommyum, and an illustrated key (in color) for determination simultaneously in English and Russian on opposite pages. In the Taxono...

Single nucleotide polymorphism datasets from 52 highly diverse accessions of the model allopolyploid plant Brassica napus.

Thomas, Schmutzer, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2015)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Variant calling has been performed with three different prediction methods using the tools FaSD, Freebayes and samtools. This allowed us to use the variant caller count (VCC) as an additional confidence value for the prediction of variant positions (VP). The VCC indicates how many variant calling methods predict the particular VP. All displayed VPs succeed in at least one of the genotypes the following criteria: bi-allelic, SNP quality score >= 100, homozygous, read depth >= 4 and a VCC >= 2....

Redundant regions in the pseudomolecules of barley cv. Morex

IBSC, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
A BED file with coordinates of redundant regions in the pseudomolecule sequence.

Animated movie of the high-resolution CT images of the developing Brassica napus seed

Verboeven, Pieter (2012)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Whole rapeseeds were scanned using a high resolution X-ray micro-CT system. The X-ray shadow projections of the 3-D object were digitized as 2048 x 2048 pixel images and were processed to obtain reconstructed cross-section images using a mathematical algorithm based on the filtered back-projection procedure implemented in the NRecon 1.6.2.0 software. This resulted in a 3-D stack of 1500 virtual sections, each consisting of 1500 × 1500 isotropic voxels of (1.7 µm3) with a linear X-ray attenuat...

15k SNP chip data for spring and winter wheat

Quddoos H. Muqaddasi, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2017)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
In total, 207 wheat genotypes (111 spring and 96 winter type) were analysed using a 15k Infinium SNP array, which is an optimized and reduced version of the 90k iSELECT SNP-chip described by Wang et al. (2014) Plant Biotechnol J 12:787-796. The development of the 15k SNP-chip and genotyping was performed by TraitGenetics GmbH (http://www.traitgenetics.com).

w7984_meraculous_scaffolds

Martin Mascher, IPK Gatersleben, Corrensstraße 3, Stadt Seeland OT Gatersleben, D-06466, Germany (2014)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Whole-genome shotgun of hexaploid wheat Synthetic W7984. The assembly was done with meraculous (Chapman et al., 2011, PLOS ONE) and consists of 6,870,110 scaffolds. The cumulative size of all scaffolds is 9,134,017,866 base pairs.

PreBreed Yield data processing scripts

Thomas, Schmutzer, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2015)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
The developed scripts (FASTQ_splitter.pl and VCF_SNP_matrix_construction.pl) were developed to assist data processing in the PreBreed Yield project. FASTQ_splitter.pl: The Perl script assists to synchronize read pairs after quality trimming. Synchronization is required after quality trimming, in case the left or the right partner of a paired end or mate pair read was removed completely. Furthermore, it can be applied to split merged FASTQ files containing the first (R1) and the second (R2) re...

Raw images files from quantitative monitoring of 484 Arabidopsis thaliana plants using high-throughput plant phenotyping

Astrid Junker, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
This dataset contains 30426 raw image files from a high-throughput plant phenotyping experiment. The growth and development of 484 Arabidopsis thaliana plants (C24 genotype) in respect to plant movement and soil cover has been monitored over 55 days. The files are described using the ISA-Tab format and fulfill the MIAPPE recommendations.

Potential contaminants in barley BAC sequence assemblies

IBSC, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
FASTA file with potential contaminant sequence (e.g. vectors, bacterial or phage sequences) that were used to screen barley BAC assemblies.