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RNA-SEQ BLOG
long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencingtechnology.
INTEGRATIVE GENOMICS VIEWER long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA HANDLING MULTI-MAPPED READS IN RNA-SEQ Many eukaryotic genomes harbour large numbers of duplicated sequences, of diverse biotypes, resulting from several mechanisms including recombination, whole genome duplication and retro-transposition LONG TERM AND SHORT-TERM EFFECTS OF RNA FIXATION ON SINGLE Cell performs various functions inside a living organism, of which development of the embryo is considered most significant as it is controlled by a cyclic series of accurate behaviors exhibited by the cell. The development of the embryo is maintained by the predilection of genes and by environmental impacts on genes. A cell is the FEATURED RNA-SEQ JOB long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA POLY-A SELECTION OR RIBO-DEPLETION? RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the methodology into the clinic is still hampered by inconsistent results from different RNA-seq protocols and involves further evaluation of its analytical reliability using patientRNA-SEQ BLOG
long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencingtechnology.
INTEGRATIVE GENOMICS VIEWER long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA HANDLING MULTI-MAPPED READS IN RNA-SEQ Many eukaryotic genomes harbour large numbers of duplicated sequences, of diverse biotypes, resulting from several mechanisms including recombination, whole genome duplication and retro-transposition LONG TERM AND SHORT-TERM EFFECTS OF RNA FIXATION ON SINGLE Cell performs various functions inside a living organism, of which development of the embryo is considered most significant as it is controlled by a cyclic series of accurate behaviors exhibited by the cell. The development of the embryo is maintained by the predilection of genes and by environmental impacts on genes. A cell is the FEATURED RNA-SEQ JOB long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA POLY-A SELECTION OR RIBO-DEPLETION? RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the methodology into the clinic is still hampered by inconsistent results from different RNA-seq protocols and involves further evaluation of its analytical reliability using patient A STEP-BY-STEP GUIDE TO SUBMITTING RNA-SEQ DATA TO NCBI The analysis of transcriptome data from non-model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is one shared feature, thegeneration of
SINGLE-CELL RNA SEQUENCING REVEALS THE CELLULAR ORIGIN AND The cell of origin and the development of breast cancer are not fully elucidated in BRCA1 mutation carriers, especially for estrogen receptor (ER)–positive breast cancers. Researchers from Peking University Cancer Hospital performed single-cell RNA sequencing (RNA-seq) on 82,122 cells isolated from the breast cancer tissues and adjacent or prophylactic normal breast tissues from four BRCA1 HANDLING MULTI-MAPPED READS IN RNA-SEQ long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA WHICH REGRESSION MODEL IS RIGHT FOR YOUR RNA-SEQ ANALYSIS Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression measurements. Although Negative Binomial (NB) regression has been generally accepted in the analysis of RNA sequencing (RNA-Seq) data, its appropriateness has not been exhaustively evaluated.RNA-SEQBLOG.COM
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SANITY – BAYESIAN INFERENCE OF GENE EXPRESSION STATES FROM Breda J, Zavolan M, van Nimwegen E. (2021) Bayesian inference of gene expression states from single-cell RNA-seq data.Nat Biotech .RNA22 VERSION 2.0
Researchers at Thomas Jefferson University present rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not rely upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA. RNA22 provides 3 different CHALLENGES IN UNSUPERVISED CLUSTERING OF SINGLE-CELL RNA Single-cell RNA sequencing (scRNA-seq) allows researchers to collect large catalogues detailing the transcriptomes of individual cells. Unsupervised clustering is of central importance for the analysis of these data, as it is used to identify putative cell types. MARGI | RNA-SEQ BLOG Bioengineers at the University of California San Diego have developed a new tool to identify interactions between RNA and DNA molecules. The tool, called MARGI (Mapping RNA Genome Interactions), is the first technology that’s capable of providing a full account__ __
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* A benchmark study of simulation methods for single-cell RNAsequencing data
* Single-cell RNA sequencing discovery of new type of stem cells leads to $2.3 million grant * Scientists identify genes involved in neuron development * pyrpipe – a Python package for RNA-Seq workflows * Scientists develop “scifi-RNA-seq” method for ultra-high-throughput RNA sequencing in single cells * Featured RNA-Seq Job – Staff Bioinformatics Scientist, RNASeq Pipelines and Applications * June 17 Webinar – Transcriptomic analysis in microphysiological models of the gut to study hypoxia and nutrient absorption * Single nuclei RNA sequencing reveals two halves of the hippocampus have different gene activity * Single-cell atlas of malaria parasite gene activity provides new targets for drugs and vaccines * Researchers curate RNA-Seq datasets to develop an interactive portal for intuitive investigation on SARS-CoV-2 relatedtranscriptomes
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A BENCHMARK STUDY OF SIMULATION METHODS FOR SINGLE-CELL RNA SEQUENCINGDATA
1 day ago Leave a comment345 Views
Single-cell RNA-seq (scRNA-seq) data simulation is critical for evaluating computational methods for analysing scRNA-seq data especially when ground truth is experimentally unattainable. The reliability of evaluation depends on the ability of simulation...Read More »
SINGLE-CELL RNA SEQUENCING DISCOVERY OF NEW TYPE OF STEM CELLS LEADS TO $2.3 MILLION GRANT 1 day ago Leave a comment301 Views
When muscle is damaged, resident stem cells mediate the repair of the injured tissue. At the same time, circulating immune cells race to thesite to...
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SCIENTISTS IDENTIFY GENES INVOLVED IN NEURON DEVELOPMENT 2 days ago Leave a comment288 Views
The study identifies RNAs not previously known in these processes, helping to better understand how the complex neuron-generation process works at the molecular level. Microscopic image of developing...Read More »
PYRPIPE – A PYTHON PACKAGE FOR RNA-SEQ WORKFLOWS 2 days ago Leave a comment501 Views
The availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. There is a pressing requirement for a framework that allows for fast, ...Read More »
SCIENTISTS DEVELOP “SCIFI-RNA-SEQ” METHOD FOR ULTRA-HIGH-THROUGHPUT RNA SEQUENCING IN SINGLE CELLS 3 days ago Leave a comment562 Views
RNA sequencing is a powerful technology for studying cells and diseases. In particular, single-cell RNA sequencing helps uncover theheterogeneity...
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FEATURED RNA-SEQ JOB – STAFF BIOINFORMATICS SCIENTIST, RNASEQ PIPELINES AND APPLICATIONS 3 days ago Leave a comment250 Views
Strong experience developing methods to analyze RNAseq datasets (including bulk RNA, single cell RNA, multi-omic analysis of RNA andDNA) and a...
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FEATURED RNA-SEQ JOB – STAFF BIOINFORMATICS SCIENTIST, RNASEQ PIPELINES AND APPLICATIONS 3 days ago Leave a comment250 Views
Strong experience developing methods to analyze RNAseq datasets (including bulk RNA, single cell RNA, multi-omic analysis of RNA andDNA) and a...
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POST-DOCTORAL POSITION IN COMPUTATIONAL BIOLOGY OF GLIOMA April 30, 2021 Leave a comment538 Views
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POST-DOC POSITION AVAILABLE – TRANSCRIPTOME BIOINFORMATICS AND RNASEQUENCING
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MAGBIO GENOMICS INC. DEVELOPS AUTOMATED RNA PURIFICATION CHEMISTRY 23 days ago Leave a comment556 Views
Mawi DNA Technologies, a biotechnology company focusing on the development of innovative technologies for biosampling, announces that MagBio Genomics has successfully developed an automated RNA purification method for iSWAB-RNA v2 ...Read More »
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MINDERA RAISES OVER $12M TO COMMERCIALIZE AN RNA SEQUENCING BASED SKINTEST
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ZYMO RESEARCH RELEASES BIOINFORMATICS PIPELINE FOR SARS-COV-2 VARIANTDETECTION
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GENEDATA SELECTOR SOFTWARE ADS NEW FUNCTIONALITY FOR SINGLE-CELL RNASEQUENCING
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ROSALIND, HELIXRUS AND GENINUS PARTNER TO BRING POWERFUL NEW SINGLE CELL ANALYSIS SERVICES TO CANCER RESEARCHERS April 20, 2021 Leave a comment758 Views
RNA-SEQ FORUM FEEDS
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correlation coefficient versus DEGs analysis: what's the best approach for low expressed genes? I have 6 folders. Each one contains 7 datasets of a specific type of cancer (RNA-Seq) and 7 datasets of… Data format for pathway based clustering of samples I came across this paper as one of the examples from this paper, this one Figure 2. Host Protein Alterations… Differential gene expression analysis of time series with replicates I have a dataset that has two groups, perturbed vs control. Each group has 3 replicates. Each replicate has 8… Why did expression based subtypng of breast cancer gain much more acceptance than others This is may not be entirely technical question but rather a academic question. But the technique behind the application is… Toptable error, wont recognize condition I am getting a rather strange error from topTable. When I run my code I get Error in fit$coefficients… Challenging benchmarks for supervised learning on sparse scRNA-seqdata
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Rip-Seq: How Do You Determine What'S Good Coverage? Hi I've performed an RNA-immunoprecipitation and then sequenced the results using NGS. We already have the reads mapped (s.cerevisiae),…
454 Normalization
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WHAT IS RNA-SEQ?
long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencing technology. The resulting sequence reads are aligned with the reference genome or transcriptome, and classified as three types: exonic reads, junction reads and poly(A) end-reads. These three types are used to generate a base-resolution expression profile for each gene. Nat Rev Genet 10(1):57-63 (2009)RECENT NEWS
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A BENCHMARK STUDY OF SIMULATION METHODS FOR SINGLE-CELL RNA SEQUENCINGDATA
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SEQUENCING OF SMALL RNAS UNDERCOVERS THEIR BIG ROLES ON GENETIC,CELLULAR LEVELS
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