Posts Tagged ‘singlecell’

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

July 2, 2016

#SingleCell Coexpression…Reveals Distinct Func. Modules [v clustering bulk RNAseq]… & Clinical Outcomes [in GBM]

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

May 7, 2016

Cell-lineage analysis in human #brain using endogenous retroelements 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

January 23, 2016

Dynamics of genomic clones in breast #cancer PDX at #singlecell resolution 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

January 13, 2016

#SingleCell #RNASeq Reveals Dynamic, Random Monoallelic Gene Expression, occurring in ~20% of genes in mice cells

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

November 14, 2015

Heterogeneity in #singlecell RNAseq…hidden subpopulations by @OliverStegle lab 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

October 23, 2015

#Singlecell ChIPseq reveals…subpopulations defined by chromatin state Sparse data: on order of 1K uniq. reads/cell

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

August 28, 2015

#SingleCell chromatin accessibility >1.6k ATAC-seq expts; many on @ENCODE_NIH cell lines H1, GM12878 & K562

L1 – Somatic – Brain – Single cell DNA

August 7, 2015

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements Somatic events from #neuron #singlecell WGS

Single cell Genome + Transcriptome Sequencing

July 28, 2015

G&T-seq: parallel…#singlecell genomes & transcriptomes by @CGATist
lab & others low cov. matched data on 130+ cells

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

August 30, 2014

#Singlecell #RNAseq highlights intratumoral heterogeneity 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