166 Works

High-throughput phenotyping reveals strong temporal dynamics of QTL action on plant growth in canola

Dominic Knoch
A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height, colour uniformity were established and...

IPK genebank accessions passport data snapshot 2019-05-15

Markus Oppermann
This data set contains a snapshot of the passport data for the current genebank collection of the IPK (status:15.05.2019). The data format follows the EURISCO MCPD, Version 2017. The data set represent the current status of the data of the Genebank Information System (GBIS). It includes information to both actively maintained and historic accessions.

Genotyping-by-sequencing SNP matrix of 243 diverse barley accessions

Martin Mascher
Genotyping-by-sequnencing (GBS) libraries were constructed for 243 barley accession. Raw reads were trimmed with with cutadapt and mapped to the draft genome assembly of barley cultivar ‘Morex’ with BWA-MEM using default parameters. SNPs were called with SAMtools 0.1.19 and filtered with an AWK script. The minimum read depth for a successful genotype calls was 10. SNPs with more than 5 % missing genotype calls were discarded. The resultant genotype matrix is accessible here as an...

Pseudomolecules and annotation of the second version of the reference genome sequence assembly of barley cv. Morex [Morex V2]

Martin Mascher
DNA sequence file in FASTA format for chromosomal pseudomolecules of barley (Hordeum vulgare) cv. Morex. This is the second release (Morex V2) of the Morex genome sequence assembly, improving on the Morex V1 release by Mascher et al. 2017, Nature [doi:10.1038/nature22043]. Sequence assembly was performed with the TRITEX pipeline (https://tritexassembly.bitbucket.io). Intermediate results (unitig, scaffold and super-scaffold sequences) are provided in the folder 'contig_and_scaffold_sequences'. The folder 'gene_annotation' holds the structural gene annotation of the Morex V2...

Whole-genome shotgun sequence assemblies of bread wheat cv. Chinese Spring and wild emmer accession Zavitan

Martin Mascher
Genome sequence assemblies in FASTA format for bread wheat (Triticum aestivum) cv. Chinese Spring and wild emmer wheat (T. turgidum ssp. dicoccoides) accession Zavitan constructed with the TRITEX pipeline (https://tritexassembly.bitbucket.io). Assemblies used Illumina paired-end and mate-pair reads generated by The International Wheat Genome Sequencing Consortium (IWGSC), Science 2018 [doi:10.1126/science.aar7191] and Avni et al., Science 2017 [doi:10.1126/science.aan0032].

BAC-based sequence scaffolds of barley cv. Morex improved by Dovetail in-vitro proximity ligation data

Martin Mascher
Genome sequence assemblies in FASTA format for barley (Hordeum vulgare) cv. Morex. Assemblies were constructed by scaffolding BAC-based sequences (Mascher et al. 2017, Nature [doi:10.1038/nature22043], sequences available from doi:10.5447/IPK/2016/30) using Chicago in-vitro proximity ligation and the Dovetail HiRise algorithm (Putnam et. al. 2016, Genome Research [doi:10.1101/gr.193474.115]). The positional information contained in the two TXT files is described in the README file.

Single-nucleotide polymorphism matrices for 403 barley genotypes (WHEALBI diversity panel)

WHEALBI Consortium
Single-nucleotide polymorphism (SNP) matrices for a diversity panel of barley (Hordeum vulgare L.) accessions belonging to the WHEALBI panel. Exome sequences that revealed substantial variation in the barley genepool were obtained and validated. Data were successfully derived for 403 genotypes from the WHEALBI research project (EU FP7 no. FP7-613556), comprising formally bred cultivars, landraces and wild barley lines. This source material represents a range of worldwide barley genetic diversity, assembled to quantify variation and explore...

Chromosome-level Assembly Reveals the Niederzenz (Nd-1) Genome Structure and Gene Set

Boas Pucker
SMRT sequencing read assemblies of Arabidopsis thaliana ecotype Nd-1 and files of the gene predictions

Variant matrix for 1,140 wild barley (Hordeum vulgare ssp. spontaneum) accessions

Steven Dreissig
Single-nucleotide polymorphism (SNP) matrices for 1,140 wild barley (Hordeum vulgare spp. spontaneum) ex situ accessions. Genotyping-by-sequencing (GBS) was performed for a total of 1,140 samples, mainly from the German federal ex situ genebank bank hosted at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, but including also samples from the Swiss and Chinese national genebanks (Mascher, 2018: http://dx.doi.org/10.5447/IPK/2018/9; derived from Milner et al. 2018, https://doi.org/10.1038/s41588-018-0266-x). Imputation of missing genotypes was performed...

Optical map of barley cv. Barke

Martin Mascher
BioNano rawdata of barley cv. Barke were assembled using the BioNano Irysview software. The assembly is provided in CMAP format. Specifications of the CMAP format are available from https://github.com/bionanogenomics/File-Format-Specification-Sheets.

Screening of wild potato genetic resources for resistance to the white potato cyst nematode

Silvia Bachmann-Pfabe
This data set contains the results of the Globodera pallida (Stone) Behrens resistance screening of wild potato accessions (Solanum spp.) during the years 2000 to 2016 maintained at the Gross Luesewitz Potato Collections (GLKS) of the IPK.

Screening of wild potato genetic resources for resistance against late blight on tubers

Silvia Bachmann-Pfabe
This data set contains results of the Phytophthora infestans (Mont.) de Bary resistance screening of wild potato accessions during the years 1995 to 2016 maintained at the Gross Luesewitz Potato Collections (GLKS) of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK).

Coding sequences and GFF3 of high confidence wild emmer genes

Sven Twardziok
This dataset contains an updated gene annotation (version 2) of 67,182 high confidence (HC) gene loci for the wild emmer genome assembly (Avni, R. et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357, 93-97 (2017)). It was done at PGSB (Helmholtz Center Munich) by Sven Twardziok for a comparative study between durum wheat (DW), Triticum turgidum L. subsp. durum and wild emmer wheat (WEW), T. turgidum subsp. dicoccoides. As...

Visualising comparative genomics with Hilbert curves

Thomas Schmutzer, Fabian Bull & Uwe Scholz
Poster - Bioinformatics of Human and Animal Genomics 2011

A case study for efficient management of high throughput primary lab data

Christian Colmsee, Steffen Flemming, Matthias Klapperstück, Matthias Lange & Uwe Scholz
Source code for the LimsLight primary data management system

IDPredictor: predict database links in biomedical database

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Supplementary material A.3 for the paper 'IDPredictor: predict database links in biomedical database'. Abstract: Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data are spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab...

Physiologische und bioanalytische Untersuchungen während der Pollenembryogenese von Hordeum vulgare

Rico Lippmann
Vergelichende Proteinanalyse ("shot gun") zwischen Pollenembryogenese nach Kältestress-Induktion und gametophytischer Entwicklung von Hordeum vulgare. Replikat 1 der Untersuchung. Nach tryptischen Verdaus erfolgte die Trennung auf einer RP18-Säule (BEH 1,7µm, 100 mm x 100 µm) gekoppelt an eine RP-18 Vorsäule (Symmetry 5µm, 20mm x 180 µm) an einer nanoLC-ESI-QTOF-MS/MS (Waters) modifiziert nach Kaspar et al. (2010). Die Auswertung der Daten Eine weitere Auswertung der Chromatogramme wurde mit dem Programm LC-MS Progenesis (Nonlinear, Großbritannien) durchgeführt.

Physiologische und bioanalytische Untersuchungen während der Pollenembryogenese von Hordeum vulgare

Rico Lippmann
Vergelichende Proteinanalyse ("shot gun") zwischen Pollenembryogenese nach Kältestress-Induktion und gametophytischer Entwicklung von Hordeum vulgare. Replikat 2 der Untersuchung. Nach tryptischen Verdaus erfolgte die Trennung auf einer RP18-Säule (BEH 1,7µm, 100 mm x 100 µm) gekoppelt an eine RP-18 Vorsäule (Symmetry 5µm, 20mm x 180 µm) an einer nanoLC-ESI-QTOF-MS/MS (Waters) modifiziert nach Kaspar et al. (2010). Die Auswertung der Daten Eine weitere Auswertung der Chromatogramme wurde mit dem Programm LC-MS Progenesis (Nonlinear, Großbritannien) durchgeführt.

IDPredictor: predict database links in biomedical database

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Abstract: Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data are spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab data, such as protein sequences, metabolites or DNA sequences as well as a...

Physiologische und bioanalytische Untersuchungen während der Pollenembryogenese von Hordeum vulgare

Rico Lippmann
Vergelichende Proteinanalyse ("shot gun") zwischen Pollenembryogenese nach Kältestress-Induktion und gametophytischer Entwicklung von Hordeum vulgare. Replikat 3 der Untersuchung. Nach tryptischen Verdaus erfolgte die Trennung auf einer RP18-Säule (BEH 1,7µm, 100 mm x 100 µm) gekoppelt an eine RP-18 Vorsäule (Symmetry 5µm, 20mm x 180 µm) an einer nanoLC-ESI-QTOF-MS/MS (Waters) modifiziert nach Kaspar et al. (2010). Die Auswertung der Daten Eine weitere Auswertung der Chromatogramme wurde mit dem Programm LC-MS Progenesis (Nonlinear, Großbritannien) durchgeführt.

Poster_BIT_IPK-Evaluation_2012

Uwe Scholz
Poster_BIT_IPK-Evaluation_2012

Poster_DI_IPK-Evaluation_2012

Swetlana Friedel
Poster_DI_IPK-Evaluation_2012

Poster_The LAILAPS Search Engine: New Features

Jinbo Chen
LAILAPS Poster für IB 2012

Distribution of ASCII characters in Database IDs

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Distribution of character frequency in sample of 51,000 IDs from 51 biomedical databases: The three columns show the ASCII code of the character, the printable form and the frequency of occurence. We hide the ASCII codes 128 - 255, because they never showed up in the sample IDs. Overall we see 182 characters do not show up in any ID (54 in the range of frequently used 7-bit ASCII subset)

Prediction performance for UniProt entry CP20C ARATH

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Evaluation of the IDPredictor ID classifier in the UniProt entry CP20C ARATH. The columns are: extracted token, predicted database cross-reference, p-value, manual evaluation (1: true posive; 0: false positive). Overall we decomposed the entry into 1,803 tokens. The table comprise only those 531 tokens which had a minimal p-value of 0.5.

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