RNA-Seq Blog - Part 768

RNA-SEQ NEWS

Fluidigm

January 13, 2010 Leave a comment 5,094 Views

Fluidigm – The C1™ Single-Cell Auto Prep System is a new approach to single-cell genomic applications, including targeted gene expression and the new mRNA sequencing protocol for transcriptome analysis of ...

Agilent Technologies

January 12, 2010 Leave a comment 4,549 Views

Agilent Technologies – Agilent’s SureSelect market leading platform provides a complete portfolio of catalog and custom products, providing the flexibility you need, for your discovery to follow-up studies. New HaloPlex ...

Epicentre (an Illumina company)

January 11, 2010 Leave a comment 7,032 Views

– The Ribo-Zero™ Magnetic Gold Kit (Epidemiology) combines Epicentre’s Ribo-Zero™ Gold (Human/Mouse/Rat) and Ribo-Zero™ (Bacteria) rRNA removal reagents into a single solution that effectively removes rRNA, including human mitochondrial RNA, ...

NuGEN Technologies

January 11, 2010 Leave a comment 4,244 Views

NuGEN Technologies – The Ovation Ultralow Methyl-Seq Library Systems provide a simple, fast and scalable solution for producing libraries used in conjunction with bisulfite sequencing to analyze DNA methylation. The ...

Kapa Biosystems

January 9, 2010 Leave a comment 5,317 Views

Depending on the enrichment or depletion strategy, RNA-Seq can be used to evaluate different populations of RNA, including total RNA, non-coding RNA (e.g microRNA, lncRNA, etc.) and mRNA. KAPA Stranded ...

Lexogen

January 9, 2010 Leave a comment 5,364 Views

Lexogen – The SENSE mRNA-Seq kit is an all-in-one library preparation protocol designed to generate Illumina-compatible libraries from total RNA within 4 hours. The SENSE protocol maintains strand-specificity and allows ...

New England Biolabs

January 8, 2010 Leave a comment 2,776 Views

The NEBNext rRNA Depletion Kit (Human/Mouse/Rat) employs an RNaseH-based method (1, 2) to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA and 28S rRNA) and mitochondrial ribosomal RNA (12S ...

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Jobs

Post-doc position available – single cell and spatial omics

May 9, 2023 Leave a comment 308 Views

Applications are invited for appointment as Post-doctoral Fellow in Single Cell and Spatial Omics in School of Biomedical Sciences (Ref.: 520386), to commence as soon as possible for two years...
Read More »
Post-doc position available – RNA Accelerator Inflammation and Immunology

March 31, 2023 Leave a comment 759 Views
Internship / Master student in single-cell RNA-seq-based expression visualization

March 10, 2023 Leave a comment 866 Views
Featured RNA-Seq Job – Bioinformatics Scientist

March 8, 2023 Leave a comment 2,268 Views
Featured RNA-Seq Job – Research Technician II – Single Cell RNA Sequencing

January 27, 2023 Leave a comment 2,780 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

Integrate bulk RNA and ATAC-seq genes

I have up and down-regulated genes from bulk RNA result from DeSeq2. Genes that are differential in chromatin accessibility between… [...]

What do the numbers mean in these RNA-Seq gene/transcript TPM files?

From the link https://gtexportal.org/home/datasets, under V7, I'm trying to do R/Python analyses on the Gene TPM and Transcript TPM files.… [...]

Getting VCF file that contain common SNPs from 6 VCF file using isec

I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all… [...]

How can I delete these lines in my fastq file?

Hi guys =) I'm sorry if this is a repeat but I haven't been able to find an answer using… [...]

What statistical test to apply for DE after CibersortX deconvolution?

This question was also asked on Biostars I am running CibersortX in high-resolution mode (which yields estimates of gene values… [...]

Salmon Pseudo count when dealing with male and female RNA-seq data

I've generated a quant seq data that I intend to use to compare male and female gene expresion, with a… [...]

Gene rank scores from LINCS database: Evangelista et al. 2022

The website https://maayanlab.cloud/sigcom-lincs/#/SignatureSearch/UpDown can be used to "Identify reversers and mimickers from over 1 million signatures by entering up and… [...]

How to use hashsolo for demultiplexing hashtags?

I am trying to use hashsolo and I want to make sure that I have done things correctly. I did… [...]

Why is there antisense sequence in RNAseq data

I'm looking at RNAseq data from CCLE. The data is paired-end. Take the cell line Hs578T and the gene HRAS… [...]

Integrating bulk RNA-Seq data with different sequencing depths and from different sources

I am attempting to integrate different bulk RNA-Seq datasets. While this is not ideal, I'm trying to reduce the technical… [...]

Test for differences between groups of samples

Sorry if the answer to this should be obvious. I have RNA-expression results from 24 samples which can be divided… [...]

How to remove orig ident. already data normalized, scaled assigned cluster/

How to remove orig ident. already data normalized, scaled assigned cluster/ Example, I have 4 sample data. like 1-control, 2-… [...]

How to differentiate DNA fastq and RNA fastq files?

I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains… [...]

RNAseq alignment: best practices for aligning to multiple isoforms?

I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed… [...]

How would you define a set of active genes from a bulk RNA-seq experiment in one biological sample? [duplicate]

I am trying to identify genes that are overall considered to be "actively transcribed" in my cell line of interest… [...]

Nextflow Error: failed to read header from "-"

I am trying to run my nextflow pipeline, and have gotten this error: samtools sort: failed to read header from… [...]

RNAseq: Why would using a more complete scaffold reduce DEGs?

I have a set of RNAseq data for a couple of relatively under-studied species. They're fungi, of the order Hypocreales.… [...]

Generating gene signature for sample classification and survival analysis patient cohort

This is from this paper The LSC17 score is calculated for each patient as a linear combination of GE of… [...]

Nextflow Pipeline: Unexpected Input "{"

I'm attempting to run a nextflow pipeline and have begun getting unexpected output for a few of the processes in… [...]

To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass… [...]

How Do I Map, Align, And Plot My Solid Results?

Hi, I recently performed an RNA immunoprecipitation followed by SOLiD sequencing (50 bp fragmented reads). I haven't received my first… [...]

Rna Data Sources???...Please Help

hi all, I would like to have your comments on data source for RNA secondary structures at CRW site http://www.rna.ccbb.utexas.edu/… [...]

Sam Format Parsing / Stats

I will need to create summaries for a bunch of SAM files produced by Tophat (RNA-Seq spliced mapping). Are there… [...]

Rna-Seq Biological Replicates...

We wish to replace microarrays with RNA-seq..we've seen papers published that specify that technical quality is quite repeatable, and thus… [...]

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

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

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.… [...]

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

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

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… [...]

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… [...]

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… [...]

Multiplexed Rnaseq

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

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… [...]

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… [...]

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)… [...]

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?… [...]

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… [...]

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… [...]

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… [...]

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… [...]