Posts Tagged ‘singlecell’

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

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells : Nature Biotechnology : Nature Publishing Group

Saturday, November 14th, 2015

Heterogeneity in #singlecell RNAseq…hidden subpopulations by @OliverStegle lab http://www.nature.com/nbt/journal/v33/n2/full/nbt.3102.html scLVM corrects for cell cycle phase

Buettner, Florian, Kedar N. Natarajan, F. Paolo Casale, Valentina
Proserpio, Antonio Scialdone, Fabian J. Theis, Sarah A. Teichmann,
John C. Marioni, and Oliver Stegle. "Computational analysis of
cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals
hidden subpopulations of cells." Nature biotechnology 33, no. 2
(2015): 155-160.

Single-cell ChIP-seq

Friday, October 23rd, 2015

#Singlecell ChIPseq reveals…subpopulations defined by chromatin statehttp://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html Sparse data: on order of 1K uniq. reads/cell

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html

Single-cell chromatin accessibility reveals principles of regulatory variation : Nature : Nature Publishing Group

Friday, August 28th, 2015

#SingleCell chromatin accessibility
http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html >1.6k ATAC-seq expts; many on @ENCODE_NIH cell lines H1, GM12878 & K562

L1 – Somatic – Brain – Single cell DNA

Friday, August 7th, 2015

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements http://www.sciencedirect.com/science/article/pii/S0896627314011374 Somatic events from #neuron #singlecell WGS

Single cell Genome + Transcriptome Sequencing

Tuesday, July 28th, 2015

G&T-seq: parallel…#singlecell genomes & transcriptomes by @CGATist
lab & others http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3370.html low cov. matched data on 130+ cells

https://twitter.com/CGATist/status/604271101678587904

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

Iain C Macaulay,
Wilfried Haerty,
Parveen Kumar,
Yang I Li,
Tim Xiaoming Hu,
Mabel J Teng,
Mubeen Goolam,
Nathalie Saurat,
Paul Coupland,
Lesley M Shirley,
Miriam Smith,
Niels Van der Aa,
Ruby Banerjee,
Peter D Ellis,
Michael A Quail,
Harold P Swerdlow,
Magdalena Zernicka-Goetz,
Frederick J Livesey,
Chris P Ponting
& Thierry Voet

Nature Methods 12, 519–522 (2015) doi:10.1038/nmeth.3370Received 18 November 2014 Accepted 27 March 2015 Published online 27 April 2015

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Saturday, August 30th, 2014

#Singlecell #RNAseq highlights intratumoral heterogeneity http://www.sciencemag.org/content/344/6190/1396.abs Subtype classifiers variably expressed across indiv. cells

Patel AP(1), Tirosh I(2), Trombetta JJ(2), Shalek AK(2), Gillespie SM(3),
Wakimoto H(4), Cahill DP(4), Nahed BV(4), Curry WT(4), Martuza RL(4), Louis
DN(5), Rozenblatt-Rosen O(2), Suvà ML(6), Regev A(7), Bernstein BE(8).

Published Online June 12 2014
Science 20 June 2014:
Vol. 344 no. 6190 pp. 1396-1401
DOI: 10.1126/science.1254257

Singled out for sequencing : Nature Methods : Nature Publishing Group

Monday, January 27th, 2014

Nice piece on #SingleCell Seq w/ implications for #cancer, neurosci, &c. Singled out for #sequencing
http://www.nature.com/nmeth/journal/v11/n1/full/nmeth.2768.html HT @naivelocus

Lots on brain, cancer & prenatal sequencing, viz:

QT:{{”
For example, as part of the Single Cell Analysis Program supported by the US National Institutes of Health Common Fund, Kun Zhang’s team will generate full transcriptomes from 10,000 cells in three areas of the human cortex. They will group the transcripts into cell
types—perhaps redefining those cell types in the process—and map the transcripts back to cortical slices of the brain. Single-cell RNA-seq itself is no longer a barrier. “If you have a good cell, and you want to get a measure of the transcriptome, there is more than one option that can lead you to that goal,” Zhang says. In general, however, extracting the neurons posthumously, minimizing RNA degradation and preserving some of the neuronal spatial information is challenging, and the group is evaluating several approaches, Zhang says.
“}}

Allele-specific expression at single cell resolution

Sunday, January 19th, 2014

QT:{{”
We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. Similar patterns of monoallelic expression were observed in mature cells. Our allelic expression analysis also demonstrates the de novo inactivation of the paternal X chromosome.
“}}

http://www.sciencemag.org/content/343/6167/193.full