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1 e compared using next-generation sequencing (RNA-Seq).
2 nt normal tissues using deep RNA-sequencing (RNA-seq).
3 d MisR-regulated genes using RNA sequencing (RNA-Seq).
4 red using next-generation sequencing of RNA (RNA-seq).
5 verse transcription (RT) such as RT-qPCR and RNA-Seq.
6 ysis of the count-based sequencing data from RNA-seq.
7 se during the preparatory steps required for RNA-seq.
8 q data, and 44 were confirmed by single cell RNA-seq.
9 els from ripe and overripe mango fruit using RNA-Seq.
10 platform for massively parallel single-cell RNA-seq.
11 wing methyl jasmonate (MeJA) treatment using RNA-seq.
13 r matrix remodeling genes, while single-cell RNA-seq analyses showed increased expression of genes re
14 small RNAs regulate mRNA fate, we conducted RNA-Seq analyses to determine not only the levels of bot
16 ital ELISA, enhanced interferon signaling by RNA-Seq analysis and constitutive upregulation of phosph
24 ion program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy br
25 retinide target genes, we performed unbiased RNA-seq analysis in liver from mice fed high-fat diet +/
26 ompasses a subset of transcripts detected by RNA-Seq analysis of in vitro-derived MK cells and that t
34 the performance and propose a comprehensive RNA-seq analysis protocol, named RNACocktail, along with
39 Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulato
51 d this, we investigated transcriptomes using RNA-seq and amino acid levels with N treatment in tea (C
53 c treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human
55 irst involves a myriad of techniques such as RNA-Seq and CLIP-Seq to identify splicing regulators and
58 ll intestine and colon organoids, along with RNA-Seq and gene ontology methods, to characterize the e
60 expression impacts other metabolic pathways, RNA-Seq and metabolite profiling were performed on stalk
64 annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDN
65 iptome-wide PE analyses to date (microarray, RNA-Seq and PAS-Seq) are NRIP1 (RIP140), a transcription
66 ression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis ag
71 ar models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately,
75 ofiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different
76 e-level correlations between RNA sequencing (RNA-seq) and microarray platforms, but have not studied
80 zygous mice compared to wild-type mice using RNA-seq; and (iii) morphological and functional conseque
82 to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzyma
83 d-factor protein capture and RNA-sequencing (RNA-seq) approach, we have assessed how mRNA association
86 b/ ), which stores and facilitates search of RNA-Seq based expression profiles available from the mod
89 ome-wide association studies (GWAS) in which RNA-seq-based measures of transcript accumulation are us
90 nced by studying single-cell RNA-sequencing (RNA-seq) but is limited by the assumptions of current an
93 g exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell w
94 ary genomic analyses such as RNA sequencing (RNA-Seq), chromatin immunoprecipitation, and ribosome pr
95 ity between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed
99 nt idea of pseudoalignment introduced in the RNA-Seq context is highly applicable in the metagenomics
101 Additionally, we tested dwgLASSO on TCGA RNA-seq data acquired from patients with hepatocellular
102 Here we describe how to apply CellNet to RNA-seq data and how to build a completely new CellNet p
103 ing the rate of differential mRNA decay from RNA-seq data and model mRNA stability in the brain, sugg
104 l splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and q
107 t combining statistical modeling with public RNA-seq data can be powerful for improving our understan
108 e wild strawberry Fragaria vesca genome with RNA-seq data derived from different stages of fruit deve
109 ociated with ceRNA's function using Geuvaids RNA-seq data for 462 individuals from the 1000 Genomes P
112 Here, by analysing 60 clinical samples' RNA-seq data from 20 HCC patients, we have identified an
113 ws the strength of combining QTL mapping and RNA-Seq data from a mouse model with association studies
114 lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves
117 quantitative trait locus analysis, utilizing RNA-seq data from human skin and found that LCE3B/C-del
118 generating ever-larger data sets comprising RNA-Seq data from hundreds or thousands of samples, ofte
120 gene expression based on the strand-specific RNA-seq data from seedling, floral bud, and root of 19 A
123 cultures and a computational analysis of SCI RNA-seq data further supported the possibility that a re
125 t and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid
127 xisting normalization methods to single-cell RNA-seq data introduces artifacts that bias downstream a
128 ped to automatically identify TUs with given RNA-seq data of any bacterium using a machine-learning a
129 ata of multiple cancer types and single-cell RNA-seq data of lung adenocarcinoma, we confirmed an ant
131 Lastly, single-nucleotide resolution of RNA-Seq data revealed 15 bicistronic and tricistronic me
133 downstream analysis of large, heterogeneous RNA-Seq data sets and we demonstrate its use with data f
136 ing data, and its implementation for several RNA-Seq data sets, as well as the whole genome sequencin
137 By analyzing over 23,000 publicly available RNA-Seq data sets, we show that Tradict is robust to noi
141 line (fibroblast) and tumor (leiomyosarcoma) RNA-seq data to compare Oncopig and human STS expression
142 We generated 27 Gb DNase-seq and 67.6 Gb RNA-seq data to investigate chromatin accessibility chan
143 cript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and
144 address challenges of analyzing large-scale RNA-seq data via several new developments to provide a c
147 ng bio-informatic comparisons of Tag-seq and RNA-seq data, and 44 were confirmed by single cell RNA-s
149 ruses, and papillomaviruses were detected in RNA-seq data, but proportions were similar (P = .73) acr
150 in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and h
157 and abundance inference from RNA sequencing (RNA-seq) data is foundational for molecular discovery.
158 bp and with this information an online Mango RNA-Seq Database which is a valuable genomic resource fo
167 It is very challenging to estimate power for RNA-Seq differential expression under complex experiment
170 suitable for single-cell RT-qPCR as well as RNA-Seq, enabling the reliable detection of cancer-speci
171 ay using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in differ
173 treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h
174 This difference allowed us to carry out RNA-seq experiments and identify a limited number of gen
179 ded support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interac
180 uce the Census algorithm to convert relative RNA-seq expression levels into relative transcript count
181 nd their microenvironments using single-cell RNA-seq from 11 primary colorectal tumors and matched no
182 ting matched whole-transcriptome sequencing (RNA-seq) from the BrainSpan project revealed varied patt
183 onal activity of 127 TFs through analysis of RNA-seq gene expression data newly generated for 448 can
184 e approach on different data sets containing RNA-seq gene transcripton and up to four ChIP-seq histon
185 genome-wide analyses utilizing ChIP-Seq and RNA-Seq, GOF p53-induced origin firing, micronuclei form
190 Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide varie
191 ise and lower coverage than traditional bulk RNA-seq, hence bringing in new computational difficultie
193 nted transcript expression using Tag-seq and RNA-seq in female rat Ventral Mesenchymal Pad (VMP) as w
194 hroid terminal differentiation, we conducted RNA-seq in human reticulocytes and identified nuclear re
195 plexed in situ hybridization and single-cell RNA-Seq in male and female mice to provide a more compre
199 y (MS) based proteomics and mRNA sequencing (RNA-Seq) in comparison to non-infectious procyclic trypa
200 zed bulk and single-cell RNA transcriptomes (RNA-seq) in SSEA4(+) hSSCs and differentiating c-KIT(+)
204 Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of
209 ation pipeline, we assembled tissue-specific RNA-Seq libraries from 113 datasets and constructed 48 3
213 tes, but the high variability of single-cell RNA-seq measurements frustrates efforts to assay transcr
214 ased on the known biotypes, all the employed RNA-Seq methods generated just a small consensus of sign
215 mmonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq dat
216 q, differential gene expression analysis for RNA-seq, nucleosome positioning for MNase-seq, DNase hyp
218 ential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a si
219 cellular adaptation to hypoxia, we performed RNA-Seq of normoxic and hypoxic head and neck cancer cel
222 Using unbiased single-cell RNA sequencing (RNA-seq) of 2400 cells, we identified six human DCs and
227 city, we performed transcriptome sequencing (RNA-seq) on two GBS strains grown under stringent respon
232 s included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metr
236 combining 14,226 single-cell RNA sequencing (RNA-seq) profiles from 16 patient samples with bulk RNA-
237 Population and single-cell RNA sequencing (RNA-seq) profiling combined with bulk assay for transpos
238 hroughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identification
248 DTU events for 8148 genes across 206 public RNA-Seq samples, and find that protein sequences are aff
250 By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression
251 ific mouse reporter strains, we performed an RNA-seq screen, identifying tip- and stalk-enriched gene
252 a novel algorithm that utilizes single-cell RNA-seq (scRNA-seq) to quantitatively measure cellular d
254 uced representation bisulfite sequencing and RNA-seq show that dCas9-SunTag-DNMT3A methylates regions
255 Differential gene expression analysis using RNA-Seq showed consistent expression of six hydrogenase
256 e accommodates both un-stranded and stranded RNA-seq so that lncRNAs overlapping with other genes can
257 d genome-wide ChIP-sequencing (ChIP-seq) and RNA-seq studies extended these findings to the in vivo s
258 nscriptional profiling, the vast majority of RNA-Seq studies typically profile only tens of samples,
260 een ectomycorrhizal partners, we performed a RNA-Seq study of transcriptome reprogramming of the basi
262 ically, we examine both short- and long-read RNA-seq technologies, 39 analysis tools resulting in 12
266 tory network, we performed a high-resolution RNA-seq time series of methyl JA-treated Arabidopsis tha
267 ifferent routes with the intent of comparing RNA-Seq to a NanoString nCounter codeset targeting 769 n
268 ile cis-regulatory elements (CREs) and using RNA-seq to characterize gene expression in the same indi
269 We performed genome-wide RNA profiling using RNA-Seq to compare the RR group and the complete remissi
270 ter) to F. pseudograminearum infection using RNA-seq to determine whether Brachypodium can be exploit
272 ompared to epidermal hair follicle stem cell RNA-Seq to identify genes representing common putative s
275 NA degradation in vivo was examined by using RNA-seq to search the H. pylori transcriptome for RNAs w
276 oal of this study was to use RNA-sequencing (RNA-seq) to analyze the host transcriptome in response t
277 e timing of zygote development and generated RNA-seq transcriptome profiles of gametes, zygotes, and
278 Here, we used shotgun proteomics, OxICAT and RNA-seq transcriptomics to analyse protein S-mycothiolat
279 h CsrA in vivo, while ribosome profiling and RNA-seq uncover the impact of CsrA on translation, RNA a
282 in late events during the viral life cycle, RNA-Seq was carried out on triplicate differentiated pop
288 Here, using protrusion-isolation schemes and RNA-Seq, we find that RNAs localized in protrusions of m
291 including in situ Hi-C, DamID, ChIP-seq, and RNA-seq, we investigated roles of the Heterogeneous Nucl
292 l ribosome affinity purification followed by RNA-Seq, we profiled astroglial ribosome-associated (pre
297 predetermined sequences, and RNA sequencing (RNA-Seq), which uses high-throughput sequencing to captu
298 have become the approach of choice prior to RNA-seq, with their efficiency varying in a manner depen
299 nificant heterogeneity in the performance of RNA-Seq workflows to identify differentially expressed g
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