RNA-Seq projects from SECARNA

The RNA Systems Biology Lab Programme compiles the different research projects developed in our lab. The RNA Systems Biology Lab is a collaborative research lab headed by PIs Margarida Gama-Carvalho and Francisco Pinto at the Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, and integrates the BioSystems and Integrative Sciences Institute (BioISI) Gene Expression and Regulation Group, headed by Margarida Gama-Carvalho. Our research brings together computational ...

Background. RB1 is a paradigm gene for heritable cancer. Almost all RB1 mutation-carriers develop retinoblastoma (heritable-Rb-patient) during childhood and many heritable-Rb-survivors develop second primary malignancies (SPMs; notably sarcomas and melanomas) throughout life, which are often fatal. To date, no standard protocols are available for early detection of SPMs. Recently, blood-based cancer tests have opened up encouraging new possibilities for surveillance. We have developed novel ...

The Collaborative Research Center / Transregio 124 Pathogenic fungi and their human host: Networks of Interaction - FungiNet studies the interaction of the human pathogenic fungi Candida albicans and Aspergillus fumigatus with their host using a Systems Biology approach. The yeast Candida albicans and the filamentous fungus Aspergillus fumigatus are by far the most important causes of life-threatening invasive mycoses in Europe. Despite the increasing incidence of these infections, the current ...

National Institute of Biology, Department of Biotechnology and Systems Biology projects

Projects that do not fall under current programmes.

Standard ASO design is based on the sequence complementarity of the oligo to its target. However, the degree of target knockdown that ASOs can achieve varies strongly between different ASOs having full complementarity to the target. To determine which factors affect the ASOs’ activity, Secarna has used a novel approach: the Company has designed and screened 51 multi-specific ASOs with a common target (IDO1, a gene involved in tryptophan metabolism), and varying numbers of diverse other targets ...

This project aims to characterise the mechanisms through which microRNAs and small non-coding RNAs act to regulate cellular processes focusing on Naïve CD4 T cell activation and viral replication - namely HIV - and to explore their potential use as a therapeutic co-adjuvant agents or targets.

Understanding the molecular basis of diseases can shed light into new methods to manage and cure diseases. Exploring the common or unique molecular mechanisms among a group of diseases may enhance our understanding of each disease or uncover therapeutic approaches that can be effective in multiple diseases. In this project we develop methods that use biological networks and known gene-disease associations to identify common molecular mechanisms associated across multiple diseases.

Aliivibrio Vl2 vs. Moritella viscosa

Vl2 vs M. viscosa

This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.

Rationale: Individuals with a cancer predisposition due to a mutation in the paradigm tumor suppressor gene RB1, have a high risk to develop the childhood cancer retinoblastoma (Rb). Biopsies are not possible in Rb, before treatment selection. Heritable Rb patients have also a high risk to develop other types of second primary, either childhood or adult, malignancies (SPMs), notably sarcomas and melanomas. Remarkably, SPMs are now the leading cause of death in heritable-Rb-survivors. Unfortunately, ...

Background: The immunoproteasome is expressed constitutively in immune cells alongside standard proteasomes and forms multiple mixed types of proteasome complexes. These mixed 20S proteasomes may have distinct proteolytic activities depending on their subunit composition and may thereby regulate immune cell function. Using site-specific versus pan-inhibitors of the immunoproteasome, we here aim to dissect the biological functions of the three active sites of the immunoproteasome for monocyte cell ...

Bistable switches are the key elements of the regulatory networks governing cell development, differentiation and life-strategy decisions. Transcriptional noise is a main determinant that causes switching between different states in bistable systems. By using the human pathogen Streptococcus pneumoniae as a model bacterium, we will investigate how transcriptional fidelity and processivity influence (noisy) gene expression and participate in bistability. To study this question, we will use both ...

The placenta remains the key to maternal diseases such as Pre-eclampsia (PE) and Intrauterine growth restriction (IUGR), however the pathophysiology of these disorders remains elusive. The aim of this study is to characterize the key proteomic variations between PE and IUGR, to better understand the pathoetiology of these diseases.Term placentas each were collected from PE, IUGR pregnancies, and age and BMI matched healthy controls. Quadrupole-orbitrap mass spectrometer was used in data dependent ...

BaCell-SysMO 2 Modelling carbon core metabolism in Bacillus subtilis – Exploring the contribution of protein complexes in core carbon and nitrogen metabolism.

Bacillus subtilis is a prime model organism for systems biology approaches because it is one of the most advanced models for functional genomics. Furthermore, comprehensive information on cell and molecular biology, physiology and genetics is available and the European Bacillus community (BACELL) has a well-established reputation for applying ...

Illumina RNA Sequencing of human PBMCs of 9 donors stimulated with two archaea, measured after 4 and 24 hours as well as without stimulation after 24 hours as control

The aim of the study is to assess the global function of RNase Y in RNA processing and degradation in Bacillus subtilis. To this end we constructed a strain allowing controlled depletion of RNase Y and used microarrays to analyze the transcriptome in response to the expression level of RNase Y.

The conditions are Control: Control (no stimulation, no TLR8 inhibition) Inhib: TLR8 inhibition Msm: Methanobrevibacter smithii stimulation Mst: Methanosphaera stadtmanae stimulation Msm_Inhib: Methanobrevibacter smithii stimulation and TLR8 inhibition Mst_Inhib: Methanosphaera stadtmanae stimulation and TLR8 inhibition

Short Name: 01_LabTrials Title: Laboratory trials Description: Selection of targets and their validation in trials performed in the laboratories and greenhouse at NIB Phenodata: ./phenodata_20210113.txt pISA Investigation creation date: 2021-01-13 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 02_FieldTrials Title: Field trials Description: Field trials - spraying CPB larvae on potato field with the insecticidal dsRNA validated for effectiveness in the laboratory trials Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: T21_SXPsysbio Title: Use a systems biology approach to identify regulatory bottlenecks in SxPv1 Description: Samples from SXPv1.0 plants as well as sister nulls (progeny from the original transgenic event in which the transgene has segregated) and wild type will be grown and leaf samples taken for RNA extraction and profiling of primary metabolites and volatiles (target pheromones as well as potential derivatives) (P1, P5). Phenotypic and GC-MS data will be obtained and analysed from ...

Aim: To provide quantitative data that will allow modeling of gene expression for all enzymes of redox metabolism and the pentose phosphate pathway. Modeling will be used to predict enzyme levels based on the integration of an RNA degradation model with translation and protein degradation rates.

Plan: The amounts of a protein in a cell can be determined by the rates of transcription, mRNA processing, translation, mRNA turnover and protein degradation. In trypanosomes analysis is simpler because ...

The raw data generated in the scope of the SysMetEx project for RNAseq, proteomics, and imaging analysis. The data was generated on single and mixed species cultures of A. Caldus, L.ferriphilum, and/or S.thermosulfidooxidans. Raw RNA data is combined in an ENA umbrella study summarising all short read data generated in the project. Raw proteomics data is provided for distinct conditions at the pride repository. Imaging data is provided for distinct conditions at a zenodo repository.

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in Urquiza-Garcia and Millar, Testing the inferred transcription rates of a dynamic, gene network model in absolute units, In Silico Plants, 2021.

Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (first version U2017.1; published as U2019.1) model, rescales ...

Data, models and simulations for the Chew et al. 2014 paper (PNAS, https://doi.org/10.1073/pnas.1410238111), using wild-type Arabidopsis ecotype Col-0 in standard 12hL:12hD growth conditions, compared to La(er) or Fei-0 accessions, or to plants overexpressing a micro RNA (miR156).

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025 doi 10.1038/s44320-025-00086-5.

Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted ...

Scope: The COVID-19 disease can have gastrointestinal manifestation. The virus replicates in the gut and has potential faecal-oral transmission besides airborne transmission (Lamers et al., 2020). Intestinal organoids are a proven experimental model of the human gut and can help understand the viral infection of the gut without animal models and additional biopsies. Single-cell RNA-seq techniques can distinguish the SARS-CoV-2 replicating cells and thus help to understand how cells respond to the ...

The P2011 model (linked in the Assay below) was rescaled to match TiMet RNA data in clock mutants from Flis et al. 2015, also linked here as separate mean and SD files. The raw TiMet data is available elsewhere on FAIRDOMHub.

The aim of the study is to assess the global function of RNase Y in RNA processing and degradation in Bacillus subtilis. To this end we constructed a strain allowing controlled depletion of RNase Y and used microarrays to analyze the transcriptome in response to the expression level of RNase Y.

Investigation files _I_01_LabTrials

Short Name: 01_TargetSelect Title: Search for genes that might be good targets for control using dsRNAs (RNAi pesticides) Description: We will examine the results of RNAi screening experiments in model organisms (e.g. Drosophila melanogaster, Tribolium castaneum) as well as employ our previous data and literature knowledge on CPB gene expression and physiology Raw Data: pISA Study creation date: 2021-01-13 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 ...

Short Name: 02_dsRNAorder Title: Ordering the production of dsRNA of selected target genes Description: In-vitro production of dsRNAs designed to silence selected CPB genes Raw Data: pISA Study creation date: 2021-01-14 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 03_dsRNAprod Title: Production of selected desigend dsRNAs in-vivo Description: We established the production of two selected designed dsRNAs in-vivo in bacterial cultures of E. coli TH115 (DE3), a strain that does not produce RNases and is thus suitable for production of long dsRNA Raw Data: pISA Study creation date: 2021-01-14 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 04_Stages Title: Expression of target genes in CPB developmental stages and body parts Description: Expression of target genes in CPB developmental stages and body parts Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 05_jun2016 Title: CPB feeding experiment jun2016 Description: Colorado potato beetle dsRNA feeding trial performed in June 2016 Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 06_oct2016 Title: CPB feeding experiment oct2016 Description: Colorado potato beetle dsRNA feeding trial performed in October 2016 Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 07_dec2016 Title: CPB feeding experiment dec2016 Description: Colorado potato beetle dsRNA feeding trial performed in December 2016 Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 08_jan2017 Title: CPB feeding experiment jan2017 Description: Colorado potato beetle dsRNA feeding trial performed in January 2017 Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 09_jun2017 Title: CPB feeding experiment jun2017 Description: Colorado potato beetle dsRNA feeding trial performed in June 2017 Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 10_apr2018 Title: CPB feeding experiment apr2018 Description: Colorado potato beetle dsRNA feeding trial performed in April 2018 Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 11_may2018 Title: CPB egg spraying experiment (dsMESH only) may2018 Description: Colorado potato beetle dsRNA egg spraying trial performed in May 2018 Raw Data: pISA Study creation date: 2021-05-10 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_02_FieldTrials

Short Name: 01_2019 Title: Field trial in the year 2019 Description: Field trial in the year 2019 Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 02_2020 Title: Field trial in the year 2020 Description: Field trial in the year 2020 Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

S.pneumoniae D39 cells (wild type and delta greA) were grown in C+Y medium and cells were harvested for total RNA isolation at mid-exponential growth (OD600nm 0.3 for wt, 0.25 for delta greA). Total RNA was isolated as described before (Kloosterman et al 2006). The total RNA samples were examined by capillary electrophoresis. dephosphorylated with antarctic phosphatase followed by treatment with polynucleotide kinase (PNK). Afterwards, samples were poly(A)-tailed using poly(A) polymerase. Then a ...

RNAseq is utilised to validate the SnpEff annotation predictions for aberrant splicing. For this purpose the percentage exon retention for exons 4, 6 and 7 are calculated using RNAseq data.

From the "data accessibility" section of Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon. (Publication):

Supplementary files have been deposited to datadryad.org under the accession: https://doi.org/10.5061/dryad.j4h65. Raw RNA-Seq data have been deposited into European Nucleotide Archive (ENA) under the project Accession no. PRJEB24480.

Dead links 2022-06-29 (the Shiny ...

RNA-seq data for In vivo 7 samples. Only 32 RNA samples from liver of male fish sequenced. Illumina poly(A)-RNA sequencing at UiB GCF, as in Yadetie et al., 2018.

Cells were seeded in 6-well plates and incubated at 37 °C and 5 % CO2 overnight. The next day, cells were washed with 1X PBS, treated with BMVs and incubated at 37 °C and 5 % CO2 for 24 h. RNA isolation was performed by using the NucleoSpin® RNA kit (MACHEREY-NAGEL, 740955.50). cDNA synthesis was performed and libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina at the Genome Analytics at Helmholtz Centre for Infection Research. Libraries were sequenced ...

Assay: _A_02.6_TransRate Short Name: 02.6_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate stat on raw tr2aacds transcriptomes Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Nonde Data: see ./input/path_to_files.txt

Short Name: 03_RNaseItreat-wet Assay Class: WET Assay Type: wet Title: RNase If treatment of dsRNA Description: RNase If treatment of dsRNA produced in-vivo pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Assay: _A_01_RNA1-RNAisol Short Name: RNA1-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation from sexy plants Description: Isolation of RNA from SxPv1.0 plants. 4 biological replicates per every included line. pISA Assay creation date: 2018-12-13 pISA Assay creator: SpelaB Lab manager: Elena Phenodata: None Featuredata: Creation date: 2018-12-13 RNA ID: $_RNA Homogenisation protocol: fastPrep Date Homogenisation: 2018-12-13 Isolation Protocol: Rneasy_Plant Date Isolation: 2018-12-13 ...

Short Name: 01_RNAseq-CLC Assay Class: DRY Assay Type: CLC Title: RNA-Seq analysis of mealybug samples from virgin and mated females Description: Mapping reads to P. citri draft genome using CLC Genomics Workbench Phenodata: ../../phenodata_20181003.txt Creation date: 2018-11-15 Data: http://stork/dirindex/fitostorage/datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/ Genome reference files: ./input/

Assay: _A_02.4_STAR Short Name: 02.4_STAR Assay Class: DRY Assay Type: STAR Title: mapping reads back to evigene .tr output Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Assay: _A_04_TransRate Short Name: 04_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate post filtering and reassignment Description: TransRate post filtering and reassignment pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Short Name: 01_RNA-Seq_dsEGFP-NGS Assay Class: WET Assay Type: NGS Title: Treatment of dsEGFP and water treated samples before sending for RNA-Seq Description: RNA-Seq DNase and cleanup of dsEGFP and water treated CPB larval samples from the june2017 experiment to determine non-specific response of dsRNA consumption pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata:

Stranded RNAseq libraries were prepared from 1µg total RNA from liver tissue using TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, USA) using double unique indices (#20022371), according to the manufacturer's instruction (Part 15031057 Rev.E). Libraries were sequenced at the Norwegian Sequencing Centre (NSC). All libraries were pooled, and the same pool was sequenced on 4 flow cell lanes on a HiSeq 3000 machine (Illumina), generating 100bp single-end reads. RNA sequencing files ...

RNAseq data for L.ferriphilum samples

Reference genome of Sulfolobus solfataricus P2 used for mapping of RNA-seq results. Based on NCBI genome of Sulfolobus solfataricus.

RNA-Seq raw data: Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose.

RNA-Seq mapping results (part1): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).

RNA-Seq mapping results (part2): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).

Excel file summarizing:

• Name of the RNAseq study
• Orion path were the .fastq files are stored
• Year the libraries were sequenced
• short description

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, ...

We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD C57BL/6J mice were fed a standard mouse chow diet and housed in a 12‐h light–dark cycle. From the age of 8 weeks, the mice were then divided into two groups of 5 mice fed with chow diet, 4 mice fed with high-sucrose diet for 3 weeks, respectively. At the age of 11 weeks, we performed a genome-wide transcriptomic analysis on tissue ...

In this study, we used publically available dataset from gene expression omnibus (GEO):

The pathophysiological mechanisms that drive non-alcoholic fatty liver disease (NAFLD) progression remain poorly understood. This multicenter study characterized the transcriptional changes that occur as liver disease progresses. 216 snap frozen liver biopsies, comprising 206 NAFLD cases with different fibrosis stages and 10 controls were studied. Samples underwent high-throughput RNA sequencing. This study ...

In this study, we used publically available dataset from gene expression omnibus (GEO):

Transcriptomic analysis of liver biopsies that cover the spectrum of nonalcoholic fatty liver disease reveals genes that are progressively regulated over the course of the disease. This study demonstrates that progressive changes in expression of these genes can be used to approximate the histological grade of a liver biopsy. Furthermore, the relative progression profiles of these disease-responsive genes are ...

CPM is a descriptive measures for the expression level of a gene.

FPKMs or Fragments Per Kilobase of exon per Million reads . Fragment means fragment of DNA, so the two reads that comprise a paired-end read count as one. Per kilobase of exon means the counts of fragments are then normalized by dividing by the total length of all exons in the gene (or transcript). This bit of magic makes it possible to compare Gene A to Gene B even if they are of different lengths. Per million reads means this value is then normalized against the library size. This bit of magic ...

Read counts for each sample

Read counts for each sample

FPKMs or Fragments Per Kilobase of exon per Million reads . Fragment means fragment of DNA, so the two reads that comprise a paired-end read count as one. Per kilobase of exon means the counts of fragments are then normalized by dividing by the total length of all exons in the gene (or transcript). This bit of magic makes it possible to compare Gene A to Gene B even if they are of different lengths. Per million reads means this value is then normalized against the library size. This bit of magic ...

Column 1: Row numbers Column 2: Sample id (See below) Column 3: Water (Fish from salt water or fresh water) Column 4: Tissue (Liver or Gut) Column 5: Feed (MA- Marine oil, VO- Vegetable oil) Column 6: Day Column 7: Count file location

Column 2 explained: The freshwater fish have no tank numbers and saltwater fish do have tank numbers eg : 69-D0-MA-G-1 - > 69 well position (id given when sequncing), Day 0, Marine oil, Gut, Fish number 1 147-D16-VO-MA-L-6 -> 147 well position, Day 16, Vegetable ...

Information on samples submitted for RNAseq

Rows are individual samples

Columns are: ID Sample Name Date sampled Species Sex Tissue Geographic location Date extracted Extracted by Nanodrop Conc. (ng/µl) 260/280 260/230 RIN Plate ID Position Index name Index Seq Qubit BR kit Conc. (ng/ul) BioAnalyzer Conc. (ng/ul) BioAnalyzer bp (region 200-1200) Submission reference Date submitted Conc. (nM) Volume provided PE/SE Number of reads Read length

Information for salmon genes, including transcript length used for calculating transcrip per million (TPM) value

First version of enzyme-constrained model (ecModel) for Streptomyces albus J1074

Preliminary metabolic network of S. pyogenes including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors. The model still needs to be validated.

First version of enzyme-constrained model (ecModel) for Escherichia coli

The novel coronavirus (SARS-CoV-2) currently spreads worldwide, causing the disease COVID-19. The number of infections increases daily, without any approved antiviral therapy. The recently released viral nucleotide sequence enables the identification of therapeutic targets, e.g., by analyzing integrated human-virus metabolic models. Investigations of changed metabolic processes after virus infections and the effect of knock-outs on the host and the virus can reveal new potential targets. Results: ...

A reconstruction of the cellular metabolism of the opportunistic human pathogen Enterococcus faecalis V583 represented as stoichiometric model and analysed using constraint-based modelling approaches

First version of Genome-scale metabolic model (GEM) for reconstraction of flavonoids biosynthetic pathways. This model includes as a chassis , the Pseudomonas Putida GEM (iJN1411) . It includes the metabolic reconstruction of more than 500 flavonoids and more than 500 reactions related to the flavonoid biosynthesis.

Genome-scale metabolic model (GEM) for Streptomyces albus, maintained on https://github.com/SysBioChalmers/Salb-GEM.

The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that ...

The new GEM of S. coelicolor developed by Tjasa Kumelj, Snorre Sulheim, Alexander Wentzel and Eivind Almaas in 2017/2018

First version of enzyme-constrained model (ecModel) for Pseudomonas putida KT2440

Stoichiometric model in SBML format using the acetate-aerobic standard scenario.

Please note that SBML was exported using the sbmlwriter class of Metano. This file was not used for the actual analyses.

Butanol producing iNS142, redesigned using RobOKoD.

E.coli Core model, with additional reactions added to generate the beta-oxadation cycle. This is the basic model used in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).

This stoichiometric model of Aromatoleum aromaticum EbN1 is a genome-scale model and comprises 655 enzyme-catalyzed reactions and 731 distinct metabolites.

The model is in the plain-text reaction format of Metano that is human-readable and can be opened with every text editor. To run this version of the model, please use the Metano Modeling Toolbox (mmtb.brenda-enzymes.org) and the associated scenario files.

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species ...

The consensus GEM for Saccharomyces cerevisiae, version 8.3.3, maintained on https://github.com/SysBioChalmers/yeast-GEM.

Standard Operating Procedure (SOP) for integration of MESI-STRAT sequence data stored in MESI-SEEK into ENA

Use this template when you upload RNA sequencing data. Email : 31 May 2016 More columns need to be added PE/SE etc?

Source: Tom Harvey [E- mail from Jon Olav 19 May 2016]