Project description:Advances in sequencing and assembly technology has led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create create vexing problems for researchers when multiple genome as-sembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells as single cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus this study highlights how the interpretation of a single cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotation, cell type identification was confounded as some classic cell type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies. To overcome the problems posed by multiple genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found this approach increased the accuracy of cell type identification and maximised the amount of data that could be extracted from our single cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single cell community is aware how genome assembly alignment can alter single cell data and its interpretation, especially when reviewing studies on non-model organisms.

2022-02-10 | GSE194093 | GEO

ESGLI Legionella data umbrella

Project description:ESGLI Legionella data collection umbrella project

| PRJEB14408 | ENA

Reference genome for Global Pneumococcal Sequence (GPS ) project

Project description:Reference genome for Global Pneumococcal Sequence (GPS ) project

| PRJEB31141 | ENA

Marine Synechococcus genome assemblies

Project description:12 new marine Synechococcus isolate genome assemblies

| PRJEB26976 | ENA

The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource. [Whole Genome Bisulfite-Seq_OX]

Project description:This data release is part of the EU BLUEPRINT reference epignome project (http://www.blueprint-epigenome.eu/) and consists of genome wide gene expression, histone modifications and DNA methylation profiles from murine Naive CD4+ T-cells and Resting B cells.

2017-12-15 | GSE94675 | GEO

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