DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

Yukselen, Onur; Turkyilmaz, Osman; Öztürk, Ahmet; Garber, Manuel; Küçükural, Alper

doi:10.1101/689539

Cited by 8 publications

(7 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Within the DolphinNext RNA-seq pipeline (Revision 4) (Yukselen et al, 2020), reads were aligned to the hg19 genome using STAR (version 2.1.6) (Dobin et al, 2013) and counts of reads aligned to RefSeq genes were quantified using RSEM (version 1.3.1) (Li and Dewey, 2011). Normalized transcript abundance in the form of TPMs were used to filter out low abundance transcripts with an average of <3 TPMs across libraries.…”

Section: Rna-seq Analysesmentioning

confidence: 99%

Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection

Silverstein

Wang

Manickas-Hill

et al. 2021

Preprint

View full text Add to dashboard Cite

BACKGROUNDRisk of severe coronavirus disease 2019 (COVID-19) increases with age, is greater in males, and is associated with decreased numbers of blood lymphoid cells. Though the reasons for these robust associations are unclear, effects of age and sex on innate and adaptive lymphoid subsets, including on homeostatic innate lymphoid cells (ILCs) implicated in disease tolerance, may underlie the effects of age and sex on COVID-19 morbidity and mortality.METHODSFlow cytometry was used to quantitate subsets of blood lymphoid cells from people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), comparing those hospitalized with severe COVID-19 (n=40) and those treated as outpatients for less severe disease (n=51). 86 healthy individuals served as controls. The relationship between abundance of specific blood lymphoid cell types, age, sex, hospitalization, duration of hospitalization, and elevation of blood markers for systemic inflammation, was determined using multiple regression.RESULTSAfter accounting for effects of age and sex, hospitalization for COVID-19 was associated with 1.78-fold fewer ILCs (95%CI: 2.34–1.36; p = 4.55 x 10−5) and 2.31-fold fewer CD16+ natural killer (NK) cells (95%CI: 3.1–1.71; p = 1.04 x 10−7), when compared to uninfected controls. Among people infected with SARS-CoV-2, the odds ratio for hospitalization, adjusted for age, sex, and duration of symptoms, was 0.413 (95%CI: 0.197–0.724; p = 0.00691) for every 2-fold increase in ILCs. In addition, higher ILC abundance was associated with less time spent in the hospital and lower levels of blood markers associated with COVID-19 severity: each two-fold increase in ILC abundance was associated with a 9.38 day decrease in duration of hospital stay (95% CI: 15.76–3.01; p= 0.0054), and decrease in blood C-reactive protein (CRP) by 46.29 mg/L (95% CI: 71.34–21.24; p = 6.25 x 10−4), erythrocyte sedimentation rate (ESR) by 11.04 mm/h (95% CI: 21.94–0.13; p = 0.047), and the fibrin degradation product D-dimer by 1098.52 ng/mL (95% CI: 1932.84–264.19; p = 0.011).CONCLUSIONSBoth ILCs and NK cells were depleted in the blood of people hospitalized for severe COVID-19, but, among lymphoid cell subsets, only ILC abundance was independently associated with the need for hospitalization, duration of hospital stay, and severity of inflammation. These results indicate that, by promoting disease tolerance, homeostatic ILCs protect against morbidity and mortality in SARS-CoV-2 infection, and suggest that reduction in the number of ILCs with age and in males accounts for the increased risk of severe COVID-19 in these demographic groups.

show abstract

Section: Rna-seq Analysesmentioning

confidence: 99%

Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection

Silverstein

Wang

Manickas-Hill

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Duplicate samples were sent for library construction and sequencing at BGI (China). Raw sequencing reads were processed using an in-house RNA-Seq data processing software Dolphin at University of Massachusetts Medical School (Yukselen et al, 2020). The raw read pairs were first aligned to C. elegans reference genome with ws245 annotation.…”

Section: Gene Expression Analysis Rna Sequencing and Analysismentioning

confidence: 99%

S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress

Godbole¹,

Gopalan²,

Nguyen³

et al. 2022

Preprint

View full text Add to dashboard Cite

Methylation is a widely occurring modification that requires the methyl donor S-adenosylmethionine (SAM) and acts in the regulation of gene expression and other processes. SAM is synthesized from methionine, which is imported or generated through the 1-carbon cycle (1CC). Alterations in 1CC function have clear effects on lifespan and stress-responsive phenotypes, but specific mechanistic links have been difficult to identify because methylation is a widely distributed modification. Here we find that two SAM synthases in C. elegans, SAMS-1 and SAMS-4, contribute differently to modification of H3K4me3, gene expression and survival in the heat stress response. Both synthases are expressed in intestinal and hypodermal cells, which are major stress responsive tissues. We find that SAM is provisioned to distinct targets, even within the same methylation mark, depending on the enzymatic source. This suggests that determining how methyl donors are provided will broaden insight into 1CC functions in aging and stress.

show abstract

“…RNA sequencing (including library construction was performed by BGI (Hong Kong). Reads were analyzed through the Dolphin analysis platform (https://dolphin.umassmed.edu/), using DeSeq to identify differentially expressed genes (Yukselen et al, 2020). Gene set enrichment was performed using WormCat (www.wormcat.com) (Holdorf et al, 2019).…”

Section: Gene Expression Analysismentioning

confidence: 99%

Stimulation of immunity-linked genes by membrane disruption is linked to Golgi function and the ARF-1 GTPase

Welsh

Smulan²,

Fanelli

et al. 2021

Preprint

View full text Add to dashboard Cite

SummaryImmune-linked genes (ILGs) are activated in response to pathogens but can also be activated by lipid imbalance. Why pathogen attack and metabolic changes both impact ILG activation is unclear. Organelles in the secretory pathway have distinct protein and lipid components and genetically separable stress programs. These stress pathways activate restorative transcriptional programs when lipid ratios become unbalanced or during dysregulated protein folding and trafficking. We find that ILGs are specifically activated when membrane phosphatidylcholine ratios change in the secretory pathway. Consistent with this result, disruption of Golgi function after RNAi targeting the ADP-ribosylation factor ARF-1 also activates ILG expression. Since increased protein secretion is altered by metabolic changes and pathogen responses, our data argue that ILG upregulation is a conserved, coordinated response to changes in trafficking resulting from intrinsic cues (lipid changes) or extrinsic stimulation (during the immune response). These findings uncover important and previously unexplored links between metabolism and the stress response.

show abstract

DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

Cited by 8 publications

References 60 publications

Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection

Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection

S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress

Stimulation of immunity-linked genes by membrane disruption is linked to Golgi function and the ARF-1 GTPase

Contact Info

Product

Resources

About