RNA-Seq Blog - Part 2

RNA-SEQ NEWS

Rapid microfluidic isolation of virally infected primary bronchial epithelial cells for single-cell RNA sequencing

Single-cell RNA sequencing (scRNA-seq) of the bronchial epithelium enables examination of cellular subtypes and their responses to viral infections. Researchers from the University of Southampton have...

Single-cell RNA sequencing reveals cells that could protect from fatal lung disease

9 days ago Leave a comment 454 Views

A subset of fibroblasts located in small foci of tissue on the edges of extensive scarring produce a protein that protects against cell aging. Single-cell RNA...

The potential of single cell small RNA sequencing

10 days ago Leave a comment 640 Views

Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, researchers first evaluate 19 protocols for single cell small RNA sequencing...

UTHSC Hosting Open Data COVID-19 RNA Sequence Resource

10 days ago Leave a comment 436 Views

Faculty members from the University of Tennessee Health Science Center have led the development of PubSeq, a global digital data repository of COVID-19 RNA sequences. PubSeq is open to all interested...

CIM-seq – an unsupervised method for physical cell interaction profiling of complex tissues

11 days ago Leave a comment 500 Views

Cellular identity in complex multicellular organisms is determined in part by the physical organization of cells. However, large-scale investigation of the...

Transcriptome-wide analysis reveals core sets of sensome and pro-inflammatory genes and their regulators

11 days ago Leave a comment 636 Views

Retinal microglial cells (RMCs) play crucial roles in maintaining normal visual functions in a healthy eye. However, the underlying mechanisms of RMCs over-activation manifesting the alterations of sensome...

Page 2 of 739«123 4 5 »10 20 30...Last »

Jobs

1 PostDoc and 2 PhDs in microRNA, scRNAseq and paleotranscriptomics

9 days ago Leave a comment 134 Views

The FrommLab is opening and recruiting 1 PostDoc (3yrs) and 2 PhDs (4yrs). to work on microRNAs in single cells, microscopic & exotic organisms and museum & permafrost samples! If ...
Read More »
Postdoctoral position on Modeling Gene Disruptions in Human Neurons

June 11, 2021 Leave a comment 495 Views
Featured RNA-Seq Job – Staff Bioinformatics Scientist, RNASeq Pipelines and Applications

June 2, 2021 Leave a comment 1,039 Views
Post-doctoral position in computational biology of glioma

April 30, 2021 Leave a comment 1,157 Views
Post-doc position available – transcriptome bioinformatics and RNA sequencing

April 12, 2021 Leave a comment 1,403 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

DESeq2. Which is better: using the altHypothesis argument in the results function or manually filtering for your desired P-value and Log2FoldChange?

In DESeq2 you can identify your differentially expressed (DE) genes using the results function. I noticed people in my lab… [...]

The confusion of using TPM (transcripts per million)

It is shown that TPM values are not suitable for DEG analysis but good for within-sample comparison since TPM normalized… [...]

Taiji doesn't run Pagerank

I'm trying to use Taiji to run a pagerank on our combined bulk RNAseq and ATACseq dataset. Here's how we… [...]

how to get normcounts for singlecellexperiment object?

I need to perform differential expression analysis using the scDD package from R, but I am not able to since… [...]

Understanding "Measurement of mRNA abundance using RNA-seq data" by Wagner et al 2012

I'm trying to understand why RPKM is not an appropriate way to normalize for RNA seq (I understand the general… [...]

Correcting for batch effect in bulk RNA seq datasets

I have samples from many different bulk RNA seq studies that exhibit an evident batch effect (samples from different labs… [...]

Combining read counts from three separate GEO studies

I want to do differential expression analysis with DESEQ2. I have three read counts files downloaded from GEO (small RNAseq… [...]

Batch effect correction using a subset of samples - using DE genes

I have some RNA-seq data with two very obvious batches as you can see in the PCA: The samples of… [...]

Installation of software Capmirseq

I am trying to install a software called Capmirseq. After installing all relevant modules I followed the installation instruction code… [...]

RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation

I have some transcriptomic (Whole) sequencing data that I should analyse. I would like to do raw data alignment to… [...]

Ccle miRna data units

Does anybody know what units the mirna expression data on ccle is in? I saw the pipeline in the original… [...]

How to create a DESeqDataSet and define experiment design before varianceStabilizingTransformation?

I have an RNAseq count matrix consisting of 2 groups (high, low) with 6 timepoints per group (T1,T2,...,T6) and 3… [...]

How does FDRtool work?

I have a question about using FDRtool. In the below code (on RNA seq data whose p values were acquired… [...]

Calculating most abundant transcript from RNA-Seq data

vcf2maf uses VEP to annotate variants, and I believe selects the default Ensembl transcript to use for annotation. Sometimes the… [...]

Get Salmon mapping/alignment summary

With HISAT2, after the alignment of fastq files you get an alignment summary like this: 20000 reads; of these: 20000… [...]

Base abbreviations other than ACTGU in sequence file

Short question: where can I find what F and J and [...]

What is the meaning of split read?

I want to use rna seq data to later perform functional tests on fusion genes. so before that I need… [...]

What are common ways to calculate gene length for TPM calculations? [duplicate]

I am aware of this similar question. But the accepted answer there answers how to calculate TPM given a mapping… [...]

RNAseq DE comparison with samples of different read length [duplicate]

I have RNA samples but with different read lengths (Eg, HiSeq 2x125 and NovaSeq 2x150bp data). I would like to… [...]

Normalize RNA seq data from multiple runs for expression analysis

I have RNA samples sequenced with TruSeq Stranded Total RNA kit protocol in Illumina HiSeq (2x125bp) and NovaSeq platforms (2x150bp)… [...]

Data Base Rna Seq Data

Hello, I am searching some RNA seq data for some while without success. Could you give me a hint where… [...]

How Many Reads Per Sample For Rna-Seq On Abi Solid

We are about to do our first RNA-seq (ABI Solid, mouse mRNA) experiment with our local genome core. They're new… [...]

Simulating Rna-Seq Reads

I'm curious if anyone has any experience simulating RNA-seq reads for aligner comparisons? I've found a software package called flux… [...]

The Rna Genes Download

Given the species below whose genomes are fully sequenced and annotated in NCBI. I only need to obtain all the… [...]

What Metrics Are Best To Describe The "Coverage" Of Rna-Seq Data?

As far as I know, DNA sequencing coverage is simply calculated as (read count x read length / genome size).… [...]

Investigating Snps Of Unknown Significance (Uv)

Hello I have available to be the entire set of SNPs of quite a few cows (don't know the precise… [...]

How To Find All Rna Stems In Genomic Data?

I am searching for RNA stems of approx. 10 to 1000 bases. Is there a fast, BLAST-like tool for scanning… [...]

Multiplexed Pair-End Sequences -- Barcode Sorting

Does there exist any tool to do barcode splitting of pair-end sequences? I realise that FastX toolkit has a barcode… [...]

Snp Analysis In 454 Sequences

Hi! I need a software to find SNPs in sequences obtained with 454 sequencing (RNA-seq). Which software would you suggest?… [...]

What'S The Difference Between 18S Rrna And 18S Rdna?

The 18S rRNA is frequently used in phylogeny (see http://en.wikipedia.org/wiki/18S_ribosomal_RNA). For example, GenBank ref. AY742884 (which I accessed from here)… [...]

Technical/Biological Replicates In Rna-Seq For Two Cell Lines

I have a question around the meaning of "biological replicate" in the context of applying RNA-seq to compare two cell… [...]

Finding Rrna Genes In Metagenomic Data

Hi all, I have 454 based metagenomic reads. I want to search for all ribosomal RNA in it is. So… [...]

Multiplexed Rnaseq

So now that Illumina HiSeq can produce a gazillion bp of sequence per lane, what's the deal with multiplexing RNA… [...]

Rna-Seq Polymorphism Detection In Non-Model Plant Organism

10 individuals (samples) will be pooled and normalized into a single library for transcriptome sequencing. The reads will be paired-end… [...]

Searching For Specific Protein Domains In Rna-Seq

Hello, I'm trying to find specific protein domains in RNA-Seq contigs to identify previously unknown isotypes. The tool which seems… [...]

Identified Potential Non-Coding Rna, And Then?

Assume we identify - by RNA-seq, tiling arrays, by prediction - possible candidate regions for non-coding, small RNAs. I wish… [...]

Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads

I'm trying to perform a spliced alignment on a limited ( [...]

Peak Detection In Intergenic Regions In Rna-Seq Data

I am currently working on RNA-seq data. One of the aims is to scan intergenic regions for transcription of e.g.… [...]

454 Normalization

Hi I have 454 results. I have list of contigs and number of reads for each time point. I need… [...]

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),… [...]

BrainSABER v0.99.5: transcriptomic similarity assessment toolkit and web application for the BrainSpan developmental dataset analysis

April 26, 2021

RNA-Seq Blog Transcriptome Research & Industry News

RNA-SEQ NEWS

Rapid microfluidic isolation of virally infected primary bronchial epithelial cells for single-cell RNA sequencing

Single-cell RNA sequencing reveals cells that could protect from fatal lung disease

The potential of single cell small RNA sequencing

UTHSC Hosting Open Data COVID-19 RNA Sequence Resource

CIM-seq – an unsupervised method for physical cell interaction profiling of complex tissues

Transcriptome-wide analysis reveals core sets of sensome and pro-inflammatory genes and their regulators

Jobs

1 PostDoc and 2 PhDs in microRNA, scRNAseq and paleotranscriptomics

Postdoctoral position on Modeling Gene Disruptions in Human Neurons

Featured RNA-Seq Job – Staff Bioinformatics Scientist, RNASeq Pipelines and Applications

Post-doctoral position in computational biology of glioma

Post-doc position available – transcriptome bioinformatics and RNA sequencing

Industry News

New England Biolabs®, Inc. Launches Primer Monitor Tool for Tracking SARS-CoV-2 Variants That May Impact Primers Used in Diagnostic Assays

Labcorp adopts Molecular Loop SARS-CoV-2 targeted RNA sequencing panel for large-scale viral surveillance

MagBio Genomics Inc. develops automated RNA purification chemistry

Mindera raises over $12M to commercialize an RNA sequencing based skin test

Zymo Research releases bioinformatics pipeline for SARS-CoV-2 variant detection

Featured Presentations

RNA Sequencing Library Preparation

RNA-targeted In Situ Sequencing for high throughput, high multiplex subcellular RNA analysis

The Concepts of Mean Fragment Length and Effective Length in RNA Sequencing

BrainSABER v0.99.5: transcriptomic similarity assessment toolkit and web application for the BrainSpan developmental dataset analysis

Introduction to scRNA-Seq Analysis

Tutorial – RNA-Seq Analysis

Demystifying pulmonary fibrosis with single cell RNA sequencing

RNA-Seq – a closer look at read mapping

Enriching pathogen transcripts from infected samples: a capture based approach to improved host-pathogen RNA-Seq

Introduction to single cell RNA sequencing data analysis

HMS Initiative for RNA Medicine

Overview of Drop-seq technology

Navigating the unCHARTed – web tool explores public sequencing data for cancer research

BARseq2 – maps neuronal projections paths and gene expression simultaneously

To splice or not to splice…

Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

New method to add “Time” resolution to your single-cell RNA-seq

A call for direct sequencing of full-length RNAs to identify all modifications

Rapid microfluidic isolation of virally infected primary bronchial epithelial cells for single-cell RNA sequencing