High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes (Q91936482)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

title

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

single cell transcriptomics

25 April 2020

main subject

1 reference

A curated database reveals trends in single-cell transcriptomics

https://www.nxn.se/single-cell-studies/data.tsv

7 February 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

Shaun Carswell

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

Kirston Barton

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

Daniel Roden

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

Fabio Luciani

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

publication date

16 July 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

published in

Nature Communications

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

page(s)

3120

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

25 April 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

23 February 2021

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

23 February 2021

https://api.crossref.org/works/10.1038%2FS41467-019-11049-4

inferred from DOI database lookup

7 January 2021

based on heuristic

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Mapping the Mouse Cell Atlas by Microwell-Seq

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Minimap2: pairwise alignment for nucleotide sequences

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Gamma-delta (γδ) T cells: friend or foe in cancer development?

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Single-cell transcriptomics to explore the immune system in health and disease

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Multiplexed quantification of proteins and transcripts in single cells

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Comprehensive single-cell transcriptional profiling of a multicellular organism.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Single-cell RNA sequencing to explore immune cell heterogeneity

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Simultaneous epitope and transcriptome measurement in single cells

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

CD49a Expression Defines Tissue-Resident CD8+ T Cells Poised for Cytotoxic Function in Human Skin

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Comparative Analysis of Single-Cell RNA Sequencing Methods.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Fast and accurate de novo genome assembly from long uncorrected reads.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Massively parallel digital transcriptional profiling of single cells

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

T cell fate and clonality inference from single-cell transcriptomes

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Deciphering the Code of the Cancer Genome: Mechanisms of Chromosome Rearrangement

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Clinical relevance of host immunity in breast cancer: from TILs to the clinic

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

IgH sequences in common variable immune deficiency reveal altered B cell development and selection

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Sources of PCR-induced distortions in high-throughput sequencing data sets

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

A complete bacterial genome assembled de novo using only nanopore sequencing data

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Spatial reconstruction of single-cell gene expression data

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Expression profiling. Combinatorial labeling of single cells for gene expression cytometry

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

PD-1 blockade induces responses by inhibiting adaptive immune resistance

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

IMGT®, the international ImMunoGeneTics information system® 25 years on.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Characterizing immune repertoires by high throughput sequencing: strategies and applications.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Improved survival with T cell clonotype stability after anti-CTLA-4 treatment in cancer patients

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Towards error-free profiling of immune repertoires.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Full-length RNA-seq from single cells using Smart-seq2.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Using synthetic templates to design an unbiased multiplex PCR assay.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Antigen-loaded MR1 tetramers define T cell receptor heterogeneity in mucosal-associated invariant T cells

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

A conserved human T cell population targets mycobacterial antigens presented by CD1b

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

IgBLAST: an immunoglobulin variable domain sequence analysis tool

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

An immune-active tumor microenvironment favors clinical response to ipilimumab

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

BLAST+: architecture and applications

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

The Sequence Alignment/Map format and SAMtools

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Alternative isoform regulation in human tissue transcriptomes

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Human alpha beta and gamma delta thymocyte development: TCR gene rearrangements, intracellular TCR beta expression, and gamma delta developmental potential--differences between men and mice

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Class-switch recombination: interplay of transcription, DNA deamination and DNA repair

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Cytoscape: a software environment for integrated models of biomolecular interaction networks

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

V(D)J Recombination and the Evolution of the Adaptive Immune System

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

The mechanism and regulation of chromosomal V(D)J recombination

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

TdT-accessible breaks are scattered over the immunoglobulin V domain in a constitutively hypermutating B cell line

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

VH and VL gene analysis in sporadic Burkitt's lymphoma shows somatic hypermutation, intraclonal heterogeneity, and a role for antigen selection

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

The role of DNA rearrangement and alternative RNA processing in the expression of immunoglobulin delta genes

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 3' ends

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Regulation of IgM and IgD synthesis in B lymphocytes. I. Changes in biosynthesis of mRNA for mu- and delta-chains

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Medullary carcinoma of breast: An immunohistochemical study of its lymphoid stroma

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Changes in J chain and mu chain RNA expression as a function of B cell differentiation

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

Analysis of cDNA clones specific for human T cells and the alpha and beta chains of the T-cell receptor heterodimer from a human T-cell line

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635368

10.1038/S41467-019-11049-4

23 February 2021

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json

25 April 2020

PubMed publication ID

31311926

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31311926%20AND%20SRC:MED&resulttype=core&format=json