[PDF] Top 20 Getting the most out of RNA-seq data analysis
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Getting the most out of RNA-seq data analysis
... unreplicated RNA-seq experiments, which are still very common among underfunded labs working with non-model organisms, may be a cost-effective way to generate candidate DEG with reasonable likelihood ... See full document
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Global Transcriptome Analysis Reveals Distinct Aluminum-Tolerance Pathways in the Al-Accumulating Species Hydrangea macrophylla and Marker Identification.
... Through RNA-seq data analysis, we constructed about 400,000 high-quality transcripts, which provided information for further investigation of the molecular mechanism of Al ... See full document
20
Identifying stably expressed genes from multiple RNA-Seq data sets
... examined RNA-Seq data on 211 biological samples from 24 different Arabidopsis experiments carried out by different ...grouped the samples according to tissue types, and in each ... See full document
26
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
... simulated data were generated using the program SynTReN (Van den Bulcke et ...enables the generation of datasets that have a distribution similar to typical microarray data, with ... See full document
19
Genome-wide analysis reveals the unique stem cell identity of human amniocytes.
... levels of stem cell markers across individual patients, we analyzed 37 RNA-seq datasets, representing 11 isolates from patients at different gestational ages and different times in ...culture. ... See full document
16
WaveSeq: a novel data-driven method of detecting histone modification enrichments using wavelets.
... detection of broad histone modification peaks. A lack of adequate validated sites for histone modification data makes it difficult to assess the performance of analysis methods ... See full document
11
WNT5A inhibits metastasis and alters splicing of Cd44 in breast cancer cells.
... from the microarray and RNA-seq experiments were compared (Figure ...compare the data, gene lists generated form Genesprings and CuffLinks had to be imported into Ingenuity ... See full document
12
Elementary screening of lymph node metastatic- related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA
... is the fifth most common cancer and the third leading cause of cancer-related deaths ...worldwide. The high mortality might be attributed to delay in detection and is closely related to ... See full document
10
Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells
... types of can- cer. In the nucleus, USP22 functions as one subunit of the SAGA to regulate gene ...However, the ge- nome-wide USP22 binding sites and its direct target genes are yet ... See full document
8
RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.
... implementations of RNA CoMPASS are also under development which will leverage large computing clouds (like Amazon EC2) and will also provide the Figure ...using RNA CoMPASS. Human transcript ... See full document
9
RNA-SEQ applied to the peacock blenny Salaria pavo: unveiling the gene networks and signalling pathways behind phenotypic plasticity in a littoral fish
... when the tide was ...to the surface, euthanized using an overdose of MS-222 (tricaine methanesulfonate anaesthetic; Sigma- Aldrich), and assigned to individual bags that were submersed on an ice bath ... See full document
308
Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells.
... filtering of genes prior to statistical testing was carried out to increase the power of detecting differentially expressed genes [10], based on the requirement that a gene have an ... See full document
20
Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.
... enable the rapid acquisition of huge amounts of genomic or transcriptomic sequence data at relatively low costs ...annotation data were available. Compared with microarrays, ... See full document
15
Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue.
... backward RNA-Seq analyses against the human transcriptome were exported from the CLC Genomics Workbench as tab-delimited text files for exploration and statistical analysis in ... See full document
16
Transcriptomic analysis of differential gene expression reveals an increase in COX2 levels during in vitro canine herpesvirus infection
... using the Total RNA Purification Kit (NorgenBiotek Corp.). The samples were incubated with deoxyribonuclease I (Invitrogen ...carried out on a 7500 Fast Real-Time PCR System (Applied ... See full document
13
ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.
... conditions. The high per-sample cost of RNA-Seq often precludes the large number of experiments needed to partition observed variance into these categories as per standard ANOVA ... See full document
15
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.
... for the same GO term evaluated (Figure 4; complete evaluation results are included in Dataset ...AUCs of 0.68, 0.70, 0.70, 0.73 and 0.76 for the five groups of multi-isoform genes, performance ... See full document
16
A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.
... cells. The transcriptome of the central cell was compared to publicly available RNA-Seq transcriptome data from various tissues and cell types of Arabidopsis ...thaliana. ... See full document
13
Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples.
... pervasiveness of this observation led us to investigate this issue using data from a variety of other publically available data ...line of investigation, we downloaded ... See full document
6
R-seqQI: RNA-Seq Quality Indicator
... progress of sequencing systems facilitates the sequencing of the genomes and transcriptomes of countless organisms on our ...measure the quality of the processed ... See full document
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