Data files

Supplementary Table S6 - EvidentialGene Summary Statistics for PacBio sequences. Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.2_assembly-contribution-count/reports/

Supplementary Table S5 - Rywal biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Rywal. Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/

Supplementary Table S4 - PW363 biological evidence filtering results. Output of 1st filtering step by biological evidence for breeding clone PW363. Layer _p_stRT/ _I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/,

Supplementary Table S3 - Désirée biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Désirée. Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/

Number of transcripts from de novo assemblies contributing to breeding clone PW363, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes.

Number of transcripts from de novo assemblies contributing to cultivar Rywal, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes, PBdn - PacBio.

In response to the COVID-19 pandemic, the Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 45,000 scholarly articles, including over 33,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.

This dataset is intended to mobilize researchers to apply recent advances in natural language processing to generate new insights in ...

First selection of LOINC Codes for data extraction

Instructions and database scripts for extracting COVID-19 related data from i2b2

Owner: Nils Gehlenborg (nils@hms.harvard.edu)

Crosslinl (URL) to Gitlab info site on COVID-19 (University Medical Center Göttingen, Department of Medical Informatics)

This Excel file contains lists of model (Comprehensive model for COVID-19) reactions and species in table format Comprehensive model for COVID-19 coused by SARS-CoV-2

This file contains description of all model parameters and corresponding references

Data curation notes provided by Alex Graf via Willi Gruissem, in addition to the PRIDE deposition.

The Excel file gives the list of samples uploaded into PRIDE. here - https://fairdomhub.org/data_files/3704

The published experimental design might lead one to expect 4x3x2x7 = 168 samples. There are more than 168 samples in the PRIDE upload for the following reasons:

First, all of the measurements from the experiment had been uploaded, including files for measurements that were repeated because of ...

This Excel file lists the samples uploaded in PRIDE. The table “Table Sorted PP and Replicates” in the Excel file has all the relevant annotation.

There are more than the expected 168 samples in the PRIDE upload for the following reasons:

First, all of the measurements from the experiment had been uploaded, including files for measurements that were repeated because of problems during the MS run. These samples are not annotated in the table. Second, we had included 4 Gold Standard samples (2 ...

Supplementary File 3 - Taxonomi cclassification of Désirée, PW363 and Rywal representative transcripts. Sequences were classified using Centrifuge and Sankey plots were generated using Pavian. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_08_cdhit_centrifuge_3cvs-GFFmerged

Supplementary File 2 - Multiple sequence alignments using ClustalOmega v1.2.1 or MAFFT v7.271 and MView v1.66. Paralogue clusters on representative and alternative sequences, at least one from each of the four genotypes. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_05_MSA_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged