RNA-Seq Blog - Part 5

RNA-SEQ NEWS

TimeTalk – decipher cell-cell communication from single-cell RNA-seq datasets

20 days ago Leave a comment 1,008 Views

Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo...

Single-nucleus RNA sequencing identifies neuronal diversity and candidate mediators of circuit assembly

25 days ago Leave a comment 380 Views

The superior colliculus (SC) is a sensorimotor structure in the midbrain that integrates input from multiple sensory modalities to initiate motor commands. It undergoes well-characterized steps of circuit...

Joint-snhmC-seq – simultaneously profile 5hmC and true 5mC in single cells

26 days ago Leave a comment 1,409 Views

Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve...

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle

26 days ago Leave a comment 747 Views

RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation...

scProjection – projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles

27 days ago Leave a comment 1,127 Views

Multi-modal single cell RNA assays capture RNA content as well as other data modalities, such as spatial cell position or the electrophysiological properties of cells. Compared to dedicated scRNA-seq...

Small RNA-Seq test could transform care for costly cattle disease

27 days ago Leave a comment 675 Views

Efforts to develop a field-side test for animal trypanosomiasis could transform management of the common, costly infection in smallholder farms...

Eye atlas pinpoints where disease-causing genes are expressed, raising hope for inroads against blindness

28 days ago Leave a comment 809 Views

Glaucoma and macular degeneration cause blindness in millions of people every year. Hundreds of genes have been implicated for increasing susceptibility to the diseases, and such genes are often starting ...

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Jobs

Data Scientist for Bioinformatics and Computer Biology

14 days ago Leave a comment 188 Views

Job Description: Ph.D. in Bioinformatics, Computational Biology, Computer Science, Biomedical Engineering, Computer Engineering, Genetics/Genomics or related field. Experience with ‘omics platform output. Experience with biological datasets and next generation sequencing ...
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Job available – Data Scientist for Bioinformatics and Computer Biology

August 21, 2023 Leave a comment 258 Views
Featured RNA-Seq Job – Bioinformatician-Computational Biologist

July 14, 2023 Leave a comment 449 Views
NERVSPAN PhD position at Single Cell Discoveries

June 15, 2023 Leave a comment 520 Views
Featured RNA-Seq Job – Team Lead Spatial Transcriptomics

June 12, 2023 Leave a comment 485 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

Working with Smart-seq3 data, have some questions regarding UMI and bar coding

Most of my experience has been working with genomic data, this time I am working on data from Smart-seq3. RNA [...]

Question about umap using different numbers of pca components as initialization

I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different [...]

scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?

I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search [...]

Paired end reads with different read lengths

I downloaded some raw RNA-seq reads from NCBI using the sra-toolkit (Accession numbers: SRR2053159-64). The reads were generated using ABI [...]

Using CSV files continaing scRNA-seq count data from GEO [closed]

I'm completely new to scRNA-seq analysis (and to most of Bioinformatics as well) so I apologize if this was asked [...]

What are the output files of RNA-Seq from facility?

This question was also asked on Reddit I am new in our lab and I am going to do bulk [...]

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions?

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length [...]

Applying glmnet to identify predictors for subtypes

I am new to glmnet and other ML techniques, so apologise in advance if this sounds a trivial question. However, [...]

Issue with Differential Gene expression analysis with Deseq2

I am using the Deseq2 package to perform a DE analysis on multiple factors. So, basically to perform the analysis [...]

DE analysis tool and method for non-coding features

I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the [...]

Feasible to find genetic variations of two samples using RNAseq data?

I have bulk RNAseq data from two strains of mice from Jackson Lab: C57BL/6 and B6.SJL. The former expresses a [...]

is it possible to count cell in Violin plot in seurat?

I tried to quantify the number of cells of Fzd9+ Macrophage. how can I know the cell count? thank you [...]

Filtering criteria for non-coding features with very low counts

I am trying to do DE analysis of non-coding features of A. thaliana. I find in the miRNA and lncRNA [...]

Statistical methods suitable for DE analysis of non coding RNAs

I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR [...]

building custom gtf file with entrez ID for any organism

How do I generate a custom gtf file format for a organism of my interest similar to human gtf file, [...]

Gene Expression Database for Psychological Disorders

Is there a comprehensive database available online of gene expression across the brain taken from individuals with psychological conditions? Resources [...]

Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs

I am writing to you to take an input or may be you can provide a different perspective. I am [...]

Looking for datasets of RNA-Seq (or scRNA-Seq) for L1 larvae C. elegans

I was wondering if anyone know of a repository for C. elegans data sets, specifically in L1 larvae stage. Are [...]

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. [...]

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 [...]