Posts Tagged ‘singlecell’

Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq

Sunday, November 3rd, 2019

https://www.biorxiv.org/content/10.1101/762773v1

New cell type analysis in human cortex

Saturday, October 26th, 2019

Published: 21 August 2019

Conserved cell types with divergent features in human versus mouse cortex

Rebecca D. Hodge, Trygve E. Bakken, Jeremy A. Miller, Kimberly A. Smith, Eliza R. Barkan, Lucas T. Graybuck, Jennie L. Close, Brian Long, Nelson Johansen, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Höllt, Boaz P. Levi, Soraya I. Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G. Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P. Gwinn, Daniel Hirschstein, C. Dirk Keene, Mohamed Keshk, Andrew L. Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G. Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V. Shapovalova, Saroja
Somasundaram, Aaron Szafer, Elliot R. Thomsen, Michael Tieu, Gerald Quon, Richard H. Scheuermann, Rafael Yuste, Susan M. Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John W. Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R. Jones, Christof Koch & Ed S. Lein

https://www.nature.com/articles/s41586-019-1506-7

Single Cell Resource for Mouse

Saturday, August 3rd, 2019

QT:{{”

Tabula Muris is a compendium of single cell transcriptome data from the model organism Mus musculus, containing nearly 100,000 cells from 20 organs and tissues. The data allow for direct and controlled comparison of gene expression in cell types shared between tissues, such as immune cells from distinct anatomical locations. They also allow for a comparison of two distinct technical approaches: “}}

https://tabula-muris.ds.czbiohub.org/

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. “}}