A Simple Guideline to Assess the Characteristics of RNA-Seq Data

Son, Keun Hong; Yu, Sungryul; Shin, Wonseok; Han, Kyudong; Kang, Keunsoo

doi:10.1155/2018/2906292

Cited by 25 publications

(15 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The majority of samples with poor replicability exhibited poor RNA transcript quality when assessed by two separate CLIA-certified labs (Fig. 1 C), particularly for the TIN metric 22 , 23 (Fig. 1 B).…”

Section: Resultsmentioning

confidence: 99%

Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples

Newton¹,

Sedgewick²,

Cisneros³

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Transcriptome profiling can provide information of great value in clinical decision-making, yet RNA from readily available formalin-fixed paraffin-embedded (FFPE) tissue is often too degraded for quality sequencing. To assess the clinical utility of FFPE-derived RNA, we performed ribo-deplete RNA extractions on > 3200 FFPE slide samples; 25 of these had direct FFPE vs. fresh frozen (FF) replicates, 57 were sequenced in 2 different labs, 87 underwent multiple library analyses, and 16 had direct microdissected vs. macrodissected replicates. Poly-A versus ribo-depletion RNA extraction methods were compared using transcriptomes of TCGA cohort and 3116 FFPE samples. Compared to FF, FFPE transcripts coding for nuclear/cytoplasmic proteins involved in DNA packaging, replication, and protein synthesis were detected at lower rates and zinc finger family transcripts were of poorer quality. The greatest difference in extraction methods was in histone transcripts which typically lack poly-A tails. Encouragingly, the overall sequencing success rate was 81%. Exome coverage was highly concordant in direct FFPE and FF replicates, with 98% agreement in coding exon coverage and a median correlation of whole transcriptome profiles of 0.95. We provide strong rationale for clinical use of FFPE-derived RNA based on the robustness, reproducibility, and consistency of whole transcriptome profiling.

show abstract

Section: Resultsmentioning

confidence: 99%

Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples

Newton¹,

Sedgewick²,

Cisneros³

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The number of mapped reads from all treatments was compared using a one way ANOVA implemented in R. FPKM values of all genes from treated and inoculated replicates were log-transformed to build PCA plots using the R-package ggfortify ( ) ( Son et al., 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Response of Brassica napus to Plasmodiophora brassicae Involves Salicylic Acid-Mediated Immunity: An RNA-Seq-Based Study

et al. 2020

View full text Add to dashboard Cite

Clubroot, caused by the obligate parasite Plasmodiophora brassicae , is an important disease of the Brassicaceae and poses a significant threat to the $26.7 billion canola/oilseed rape ( Brassica napus ) industry in western Canada. While clubroot is managed most effectively by planting resistant host varieties, new pathotypes of P. brassicae have emerged recently that can overcome this resistance. Whole genome analyses provide both a toolbox and a systemic view of molecular mechanisms in host-pathogen interactions, which can be used to design new breeding strategies to increase P. brassicae resistance. We used RNA-seq to evaluate differential gene expression at 7, 14 and 21 days after inoculation (dai) of two B. napus genotypes with differential responses to P. brassicae pathotype 5X. Gall development was evident at 14 dai in the susceptible genotype (the oilseed rape ‘Brutor’), while gall development in the resistant genotype (the rutabaga ( B. napus ) ‘Laurentian’) was limited and not visible until 21 dai. Immune responses were better sustained through the time-course in ‘Laurentian’, and numerous genes from immune-related functional categories were associated with salicylic acid (SA)-mediated responses. Jasmonic acid (JA)-mediated responses seemed to be mostly inhibited, especially in the resistant genotype. The upregulation of standard defense-related proteins, like chitinases and thaumatins, was evident in ‘Laurentian’. The enrichment, in both host genotypes, of functional categories for syncytium formation and response to nematodes indicated that cell enlargement during P. brassicae infection, and the metabolic processes therein, share similarities with the response to infection by nematodes that produce similar anatomical symptoms. An analysis of shared genes between the two genotypes at different time-points, confirmed that the nematode-like responses occurred earlier for ‘Brutor’, along with cell metabolism and growth changes. Additionally, the susceptible cultivar turned off defense mechanisms earlier than ‘Laurentian’. Collectively, this study showed the importance of SA in triggering immune responses and suggested some key resistance and susceptibility factors that can be used in future studies for resistance breeding through gene-editing approaches.

show abstract

“…Principal component analysis of the adipocytes revealed clustering of the diet groups and timepoints. This analysis facilitates a high level overview of similarities and differences between the samples and groups in relation to how they cluster 44 (Fig. 3A).…”

Section: Adipocytes Upregulate Expression Of Extracellular Matrix Genmentioning

confidence: 99%

The Adipocyte Acquires a Fibroblast-Like Transcriptional Signature in Response to a High Fat Diet

Jones

Rabhi

Orofino

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Visceral white adipose tissue (vWAT) expands and undergoes extensive remodeling during diet-induced obesity. Much is known about the contribution of various stromal vascular cells to the remodeling process, but less is known of the changes that occur within the adipocyte as it becomes progressively dysfunctional. Here, we performed a transcriptome analysis of isolated vWAT adipocytes to assess global pathway changes occurring in response to a chronic high fat diet (HFD). The data demonstrate that the adipocyte responds to the HFD by adopting a fibroblast-like phenotype, characterized by enhanced expression of ECM, focal adhesion and cytoskeletal genes and suppression of many adipocyte programs most notably those associated with mitochondria. This study reveals that during obesity the adipocyte progressively becomes metabolically dysfunctional due to its acquisition of fibrogenic functions. We propose that mechano-responsive transcription factors such as MRTFA and SRF contribute to both upregulation of morphological genes as well as suppression of mitochondrial programs.

show abstract

A Simple Guideline to Assess the Characteristics of RNA-Seq Data

Cited by 25 publications

References 20 publications

Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples

Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples

Response of Brassica napus to Plasmodiophora brassicae Involves Salicylic Acid-Mediated Immunity: An RNA-Seq-Based Study

The Adipocyte Acquires a Fibroblast-Like Transcriptional Signature in Response to a High Fat Diet

Contact Info

Product

Resources

About