Data files

Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD+ in medium-chain acyl-CoA dehydrogenase knockout mice. During fasting, mitochondrial fatty-acid β-oxidation (mFAO) is essential for the generation of glucose by the liver. Children with a loss-of-function deficiency in the mFAO enzyme medium-chain acyl-Coenzyme A dehydrogenase (MCAD) are at serious risk of life-threatening low blood glucose levels during fasting in combination with intercurrent disease. However,
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Number of transcripts from de novo assemblies contributing to cultivar Désirée, 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.

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
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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
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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 Table S8 - Read count summary for Désirée drought samples mapped to the representative Phureja DM and Désirée reference transcriptomes.
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Supplementary Figure 3 - Venn diagrams showing the overlap of paralogue clusters in cultivar-specific transcriptomes and merged Phureja DM gene model.
Representatives and alternatives of the stPanTr (pan-transcriptome) paralogue cluster are counted as well as alternatives defined at stCuSTr (cultivar-specific transcriptome) step. For Phureja, the merged ITAG and PGSC DM gene models were counted.
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Supplementary Table S7 - Paralogue cluster information of cultivar-specific and pan-transcriptome sequences extended with annotations and quality classification.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged/reports

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 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

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