Posts Tagged ‘singlecell’

Human Cell Atlas Method Development Community timeline

Sunday, April 7th, 2019

https://www.protocols.io/groups/hca

UMAPs

Sunday, March 3rd, 2019

A lineage-resolved molecular atlas of C elegans embryogenesis at #singlecell resolution, w/ @JIsaacMurray, @JunhyongKim, @ColeTrapnell & B Waterston https://www.BiorXiv.org/content/10.1101/565549v1 Compares the known cell lineage of the worm to trees based on UMAP cell-type clusters. Remarkable agreement

https://twitter.com/MarkGerstein/status/1101927645145645056

A single-cell molecular map of mouse gastrulation and early organogenesis | Nature

Friday, March 1st, 2019

https://www.nature.com/articles/s41586-019-0933-9

The single-cell transcriptional landscape of mammalian organogenesis

Friday, March 1st, 2019

Using single-cell combinatorial indexing, we profiled the
transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment.

https://www.nature.com/articles/s41586-019-0969-x.epdf

Everyday Scientist » deconvoluting deconvolving

Sunday, January 14th, 2018

http://blog.everydayscientist.com/?p=517

A survey of human brain transcriptome diversity at the single cell level

Wednesday, June 28th, 2017

Brain #transcriptome diversity at the single cell level
http://www.PNAS.org/content/112/23/7285 Has useful gene-exp. profiles of specific neural cell types

has profiles for 185 biomarker genes for 6 cell types

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes

Saturday, July 2nd, 2016

#SingleCell Coexpression…Reveals Distinct Func. Modules [v clustering bulk RNAseq]… & Clinical Outcomes [in GBM]
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004892

QT:{{”
We found that the co-expressed genes observed in single cells and bulk tumors have little overlap and show distinct characteristics. The co-expressed genes identified in bulk tumors tend to have similar biological functions, and are enriched for intrachromosomal
interactions with synchronized promoter activity. In contrast, single-cell co-expressed genes are enriched for known protein-protein interactions, and are regulated through interchromosomal interactions. “}}

Cell lineage analysis in human brain using endogenous retroelements. – PubMed – NCBI

Saturday, May 7th, 2016

Cell-lineage analysis in human #brain using endogenous retroelements http://www.cell.com/neuron/abstract/S0896-6273(14)01137-4 Tracing L1 insertions w/ #singlecell sequencing

Using single cell WGS of 16 neuronal cells the authors investigated two somatic insertions of L1Hs elements in an adult human brain. Using these results the authors infer that L1 somatic insertions are infrequent and ALUs and SVAs somatic retrotransposition are extremely rare. Assessing two L1Hs insertions in 32 samples across different regions of this same adult brain, they found that while one insertion was spatially restricted (2x1cm region), the other was found across all samples of the adult brain (but not found in other tissues such as Heart, Lung, etc.). The more restricted one (L1Hs#1) is inferred to have happened during the Fetal stage (first trimester) while the broader one happened earlier, approximately 2 weeks
post-fertilization. Overall the paper is clear, concise, and simple. It answers an interesting biological question: Can retrotransposition be used as a marker of cell clonal expansion? It does, although the retrotransposition frequency is very small and SNVs might support better results for the same analysis due to their higher frequency..

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution : Nature : Nature Publishing Group

Saturday, January 23rd, 2016

Dynamics of genomic clones in breast #cancer PDX at #singlecell resolution http://www.nature.com/nature/journal/v518/n7539/full/nature13952.html Extensive trees of samples & some WGS

Peter Eirew,
Adi Steif,
Jaswinder Khattra,
Gavin Ha,

Jazmine Brimhall,
Arusha Oloumi,
Tomo Osako
et al.

Nature 518, 422–426 (19 February 2015) doi:10.1038/nature13952

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells | Science

Wednesday, January 13th, 2016

#SingleCell #RNASeq Reveals Dynamic, Random Monoallelic Gene Expression, occurring in ~20% of genes in mice cells
http://science.sciencemag.org/content/343/6167/193.abstract