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 ...

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.

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 ...

An exploration on gene expression data was carried out on single-cell RNAseq analyses of bronchoalveolar lavages from nine COVID-19 patients, three moderate cases, one severe case and five critical cases (GSE145826) (doi: 10.1038/s41591-020-0901-9). To these data, single-cell RNA-sequencing from one COVID-19 lung biopsy, ~10 weeks after initial infection was added to represent persistent severe COVID19 patient group (3 weeks after symptom onset) (GSE163919). For this analysis, the epithelial cell ...

Aim: To investigate whether Atlantic cod that feed close to aquatic breeding facilities are affected by chlorpyrifos-methyl. Feeding experiment with chlorpyrifos-methyl, an organophosphorous pesticide detected in plant based salmon feed. Based on previous experiments using salmon.

Doses: 0, 0.5, 5.0, 25 mg/kg) chlorpyrifos-methyl. Duration: 30 days Set-up: Three tanks per treatment (12 in total)

Samples include: Liver, plasma, bile, brain. Analysis include:

• Have RNAseq and metabolomics from 36 ...

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 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.

RNAseq data for L.ferriphilum samples

Rawdata for RNAseq derived from biofilms on chalcopyrite grains

Link to RNAseq raw data

RNAseq raw data derived from continuous culture samples

An overview of RNA sequencing data generated in GenoSysFat (and a couple of others).

Source: Email from Simen Rød Sandve to Jon Olav Vik and Fabian Grammes 2017-02-10, titled "RNAseq generert i GSF".

This should be turned into separate RNAseq Assays when we can allocate people for it. Currently the following have records already:

Tissue panel for gene expression in ZF, Med, RT https://fairdomhub.org/assays/324

Tissue panel for gene expression in ZF,Med,RT- RNA sequencing https://fairdomhub.org/assays/395 ...

Short Name: 04_mapReadsToAs2-STAR Assay Class: DRY Assay Type: STAR Title: Map RNAseq reads to de-novo assembly2 Description: STAR mapper was used to map back P citri RNAseq reads used for generation the de-novo assembly2. pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Data derived from RNAseq

The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length

Short Name: 08_mapReadsToAs1-STAR Assay Class: DRY Assay Type: STAR Title: Map RNAseq reads to de-novo assembly1 Description: STAR mapper was used to map back P citri RNA-Seq reads used for generation of the de-novo assembly1. Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Short Name: 02_CLC-RNASeq Assay Class: DRY Assay Type: RNASeq Title: CLC RNA-Seq data analysis dsEGFP vs water treatment Description: CLC RNA-Seq data analysis dsEGFP vs water treatment pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 04_SxPv12_GeneSetEnrichment-RNAseg-GSEA Assay Class: DRY Assay Type: RNAseq-GSEA Title: GSEA of SxPv1.2 expression data Description: GSEA anaylysis with MapMan3 BINs as gene sets and SxPv1.2 logFC data. pISA Assay creation date: 2021-11-24 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

This assay is designed to measure the decay kinetics of mRNA in T. brucei blood forms. T. brucei lacks the canonical transcriptional regulation employed by other eukaryotes through transcription factors, and relies almost entirely on regulation of mRNA decay and further downstream steps in order to control gene expression. 3 replicates of 8 time points were taken to measure mRNA abundance in the cell using RNA-seq. The first time point was fot WT, untreated cells; the second was 5 min after the ...

Short Name: SxPv12ScreeningT2-GCMS Assay Class: WET Assay Type: GCMS Title: Screening of sex pheromone production in SexyPlant v1.2 T2 transgenic generation for further RNASeq analysis. Description: The purpose of this study is to screen the population of T2 transgenic generation of SxPv1.2, to analyze the production of moth sex pheromones in these plants and be able to choose from them the most interesting ones in terms of production for further RNASeq analysis. pISA Assay creation date: 2021-12-09 ...

RNAseq data file, Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/samples_ELOVL2/splicing/elovl2.splicing.txt

Umbrella study for all RNAseq rawdata Separate projects can be accessed under "component projects"

Excel file summarizing:

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

Overivew of RNAseq and proteomics samples with respective accessions to access the raw data on ENA or PRIDE respectively.

Information for RNA and protein samples and cultures they were derived from.

Table combining data for L.ferriphilum. RNAseq data, Proteomics LFQs, Functional annotation

The file contains the normalized relative read counts (RPM) of 2 mRNA decay experiments. Columns in blue correspond to experiment 1, columns in violet correspond to experiment 2. The time points are in column headers. The last 3 columns contain parameters and half lives calculated from an exponantial fit of all data points. Normalization was done in 2 steps :first by calculating RPM i.e. reads per million of aligned reads to unique ORFs, second by normalizing this to the total amount of mRNA ...

Overview of the quality control for the RNAseq short read data before quality filtering of the reads

Overview of the quality control for the RNAseq short read data after quality filtering of the reads

Repository for code used in data analysis (mainly for RNAseq) and for generating summary tables and overviews.

Spreadsheet of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater).

Spreadsheet columns are:

• Date (YYYY-MM-DD)
• Day (day zero is the day before first feeding with new feed)
• Inputter (person entering data into Excel)
• Tank (1, 2, 4, 5 with Atlantic salmon, 3 and 6 with rainbow trout)
• Section (tanks were divided in half using perforated walls)
• Treatment (explained in sheet "treatments")

...

_p_RNAinVAL/_I_03_Omics/_S_01_ns-dsRNA_trans/_A_02_CLC-RNASeq/

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

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]

For the study of mRNA decay rates, transcription was inhibited with ActinomycinD, and RNA splicing with Sinefungin, at different time points, in the Matthews lab. rRNA depleted RNA was extracted from each of the samples in the Clayton lab, and sent for deep sequencing at the BioQuant facility in Heidelberg

This protocol describes the analysis of RNA-Seq data to identify differential expressed genes between two samples. The protocol is simply the analysis of the data and do not include the sequencing protocol.

The procedure describes the preparation of fluorescent DNA probes from human mRNA or total RNA.

_p_RNAinVAL/_I_03_Omics/_S_01_ns-dsRNA_trans/_A_02_CLC-RNASeq/

_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_08_SelTargetsA-dry/

_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_08_SelTargetsA-dry/

_p_SUSPHIRE/_I_T21_SXPsysbio/

_p_SUSPHIRE/_I_T21_SXPsysbio/

_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1/

_p_SUSPHIRE/_I_T21_SXPsysbio/

_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_08_SelTargetsA-dry/

_p_SUSPHIRE/_I_T21_SXPsysbio/

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-oldG-DE/_A_07_transgenes-CLC/

_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_08_SelTargetsA-dry/

_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_genome/_A_01_RNAseq-CLC/