RNA-Seq projects from SECARNA

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 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 ...

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 ...

Aliivibrio Vl2 vs. Moritella viscosa

Vl2 vs M. viscosa

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, ...

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 ...

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.

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 ...

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 ...

Short Name: P4_SxP10-oldG-DE Title: SxPv1.0 RNA-seq analysis using old Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the published (old) genome of Nicotiana benthamiana. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: No

Short Name: P4_SxP10-newG-DE Title: SxPv1.0 RNA-seq analysis using the new Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the not yet published now high quality genome of Nicotiana benthamiana from the Newcotiana project. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

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 ...

Short Name: P4_Pcitri_tr2 Description: Study of P. citri transcriptome data from SUSPHIRE and mealybug.org RNA-Seq datasets Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Lauren Baugh, Brittany A. Goods, Juan S. Gnecco, Yunbeen Bae, Michael Retchin, Constantine N. Tzouanas, Megan Loring, Keith Isaacson, Alex K. Shalek, Douglas Lauffenburger, Linda Griffith

https://www.medrxiv.org/content/10.1101/2022.01.29.22269829v1

Endometriosis is a debilitating gynecological disorder affecting approximately 10% of the female population. Despite its prevalence, robust methods to classify and treat endometriosis remain elusive. Changes ...

Kathryn M. Yammine, Sophia Mirda Abularach, Michael Xiong, Seo-yeon Kim, Agata A. Bikovtseva, Vincent L. Butty, Richard P. Schiavoni, John F. Bateman, Shireen R. Lamandé, and Matthew D. Shoulders

A dbGaP Submission is underway and metadata will be updated at the completion of submission. The remaining of the data and metadata are available here.

DOI: 10.1101/2024.11.07.622468.

Abstract:

Objectives Mutations in the procollagen-II gene (COL2A1) ...

Short Name: P1_SPv10T2andT3 Title: Characterization of SPv1.0 plants of the T2 and T3 generations Description: Plants of the SxP v1 second and third generation were grown in the greenhouse and leaf samples were collected for analysing their metabolome (via GC-MS) and transcriptome (via RNA-seq). Phenotypic data such as plant height was also recorded. Raw Data: pISA Study creation date: 2018-11-09 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative Commons Attribution ...

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 ...

Single-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to “low quality” potentially leading to data misinterpretation. Common standard quality control parameters involve the ...

Joshua D. Bromley, Sharie Keanne C. Ganchua, Sarah K. Nyquist, Pauline Maiello, Michael Chao, H. Jacob Borish, Mark Rodgers, Jaime Tomko, Kara Kracinovsky, Douaa Mugahid, Son Nguyen, Dennis Wang, Jacob M. Rosenberg, Edwin C. Klein, Hannah P. Gideon, Roisin Floyd-O’Sullivan, Bonnie Berger, Charles A Scanga, Philana Ling Lin, Sarah M. Fortune, Alex K. Shalek, JoAnne L. Flynn

Link to Paper: https://www.cell.com/immunity/fulltext/S1074-7613(24)00375-3

Immunological ...

Lindsay B Volk, Monét Norales, Callie Karjane, Joshua J Corrigan, Alper J Alcaraz, Lee J Pribyl, Nicolette A Bugher, Megan Blawas, Isabella Dulski, Einthavy Arunachalam, Nina Gubina, Emily Michelsen, Kannammai Pichappan, Natalya Yakimchuk, Matilda Swanson, Duanduan Ma, Stuart S Levine, Desiree L Plata, Robert G Croy, Leona D Samson, John M Essigmann, Carole L Yauk, Sebastian E Carrasco, Bevin P Engelward

Abstract: N-Nitrosodimethylamine (NDMA) is a probable human carcinogen found in ...

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.

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/

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

Rawdata for RNAseq derived from biofilms on chalcopyrite grains

Link to RNAseq raw data

RNAseq raw data derived from continuous culture samples

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 ...

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:

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 ...

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 ...

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:

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.

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 ...

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:

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

A list of interesting lipid genes

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

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).

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, ...

Excel file summarizing:

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

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 ...

Single nuclei transcriptomics data as .csv files from the Allen Brain atlas data set of mus musculus (https://celltypes.brain-map.org/) have been utilized as an input for scSynO. The underlying analysis is part of the manuscript entitled "Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling". Data anaylsis and visalizations were mainly generated with the Seurat R package (https://satijalab.org/seurat/archive/v3.2/spatial_vignette.html)

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?

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.

This file contains the detailed experimental protocol to isolate nuclei from murine hearts.

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

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

This file contains the detailed experimental protocol for the cultivation of "induced sinoatrial bodies (iSABs), the scRNA-Seq procedure as well as the general computational workflow for data processing. The R-script is provided separately.

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

Presentation at the SysMO-LAB2 meeting in Copenhagen November 2012. Group from Nofima/Norwegian University of Life Sciences, Ås, Norway. Work on four strains of Lactobacillus plantarum, omics-analyses, diversity.

_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_genome/_A_02_limma-R/

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

_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_genome/_A_03_limma_min50counts-R/

_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_01_jun2016-phenotyping/

_p_SUSPHIRE/_I_T21_SXPsysbio/

_p_RNAinVAL/_I_03_Omics/_S_01_ns-dsRNA_trans/_A_01_RNA-Seq_dsEGFP-NGS/

_p_RNAinVAL/_I_03_Omics/_S_01_ns-dsRNA_trans/_A_01_RNA-Seq_dsEGFP-NGS/

_p_SUSPHIRE/_I_T21_SXPsysbio/

_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_genome/_A_01_RNAseq-CLC/

_p_SUSPHIRE/_I_T21_SXPsysbio/

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

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

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

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

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

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

_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_genome/_A_01_RNAseq-CLC/

_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_genome/_A_01_RNAseq-CLC/