Holger Heyn
Single-Cell Genomics Researcher . Looking for answers in the human genome. Barcelona, SPAIN.
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Improving oligo-conjugated antibody signal in multimodal single-cell analysis
bioRxiv 21d 3 tweets
Simultaneous measurement of surface proteins and gene expression within single cells offers high resolution snapshots of complex cell populations. These methods rely on staining cells with oligo-conjugated antibodies analogous to staining for flow-...
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Holger Heyn COST-EFFECTIVE #singlecell antibody sequencing with CITEseq. Less antibodies, smaller volumes, fewer reads in empty drops --> better signal-to-noise ratio and reduced sequencing and reagent costs! Even better combined with smart sample multiplexing! 20d
Single cell profiling of total RNA using Smart-seq-total
bioRxiv 34d 2 tweets
The ability to interrogate total RNA content of single cells would enable better mapping of the transcriptional logic behind emerging cell types and states. However, current RNA-seq methods are unable to simultaneously monitor both short and long,...
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Holger Heyn After Smart-seq1/2/3/+/v4, now Smart-seq-total from the Quake lab. #singlecell profiling of total RNA, coding and non-coding. "We show that cell types can be distinguished based on the abundance of non-coding transcripts alone" 34d
SPOTlight:Seeded NMF regression to Deconvolute Spatial Transcriptomics Spots with Single-Cell Transcriptomes
bioRxiv 34d 2 tweets
The integration of orthogonal data modalities greatly supports the interpretation of transcriptomic landscapes in complex tissues. In particular, spatially resolved gene expression profiles are key to understand tissue organization and function....
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Holger Heyn READY FOR PRIME TIME! Proud to present: SPOTlight: Seeded NMF regression to Deconvolute Spatial Transcriptomics Spots with #singlecell Transcriptomes Advancing Digital Patholgy w/ #ST #visium @10xGenomics. 34d
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer
Nature Genetics 44d 3 tweets
Single-cell RNA sequencing of colorectal tumors highlights associations between lineage-related gene expression signatures and specific stromal and immune cell populations.
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Holger Heyn A detailed #singlecell map of the tumor microenvironment #TME and cancer cell heterogeneity of colorectral cancer #CRC. Great resource to further explore. 43d
Sampling time-dependent artifacts in single-cell genomics studies
Genome Biology 57d 2 tweets
Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid,...
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Holger Heyn WARNING. Prolonged sampling time affects #singlecell RNAseq and scATACseq studies. Ensure standarsized sample handling for clinical and biobank cohorts. HERE we provide practical solutions 👇 Thanks for being efficient and quick. 57d
Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis
Communications Biology 62d 3 tweets
Maeve O’Huallachain et al. report a method that enables simultaneous, ultra-high throughput single-cell barcoding for targeted single-cell protein and RNA analysis. They show the utility of their method in analyses of mRNA and protein expression in...
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Holger Heyn That looks very interesting! Split-pool antibody and targeted RNAseq for scalable (millions) #singlecell analysis by . 62d
Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19
medRxiv 64d 2 tweets
The clinical course of COVID-19 is highly variable, however, underlying host factors and determinants of severe disease are still unknown. Based on single-cell transcriptomes of nasopharyngeal and bronchial samples from clinically well-characterized...
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Holger Heyn IMPRESSIVE tour-de-force #singlecell study on #COVID19 patients with @10xGenomics at BSL3. Nasopharyngeal and bronchial sampling from patients with moderate and critical severities. Great example for speedy collaborative science . 64d
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes
Nature Methods 65d 2 tweets
Souporcell clusters single-cell RNA-seq data using genotype information without the use of a genotype reference.
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Holger Heyn Doublet? Ambient RNA? Unlimited multiplexing? Souporcell: The multi-tool for scalable, clean #singlecell studies using reference-free cell/read genotyping. 65d
Single-cell RNA counting at allele and isoform resolution using Smart-seq3
Nature Biotechnology 65d 10 tweets
Smart-seq3 enables isoform- and allele-specific reconstruction of RNA molecules.
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Holger Heyn IT IS OUT . Super-sensitive #singlecell RNAseq with Smart-seq3. Full-length transcriptome and very deep phenptyping information. We all shouldn't use anything else from now on. Congrats ! 65d
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
Nature Biotechnology 93d 6 tweets
A multicenter study compares 13 commonly used single-cell RNA-seq protocols.
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Holger Heyn OUT NOW! So proud to present our #benchmarking of #scRNAseq methods . Studies led by . Back-to-back effort w/ and coordinated . In this thread our take-home messages as joint Tweetorial 93d
Science in the time of coronavirus
Nature Methods 97d 1 tweets
Despite the incredible challenges, the science research community is stepping up to address the coronavirus pandemic in multiple ways.
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Holger Heyn "If this current crisis has any silver lining, we are hopeful that basic scientific research will emerge stronger, more collaborative, more transparent, better funded and more respected by the public than ever." by 97d
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
bioRxiv 117d 4 tweets
Experimental single-cell approaches are becoming widely used for many purposes, including investigation of the dynamic behaviour of developing biological systems. Consequently, a large number of computational methods for extracting dynamic...
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Holger Heyn #singlecell RNAvelocity outputs are sensitive to preprocessing (exon/intron counts). Differences in quantification can "have a large effect on estimated velocities as well as the biological interpretation." Benchmarking by 98d
TUTORIAL for single-cell RNA/ATAC sequencing
Google Docs 103d 1 tweets
Dear Single-Cell community, After weeks of fruitful discussion on #sc RNA seq and #scATAC-seq experimental designs in our single-cell QA #scQA forum, we are now launching the NEXT STEP towards a high-quality data production for the community! With...
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Holger Heyn Dear Single-Cell community, After weeks of fruitful discussion on #scRNAseq #scATACseq experimental designs in our #singlecell #scQA forum, we are now launching the NEXT STEP. We write a TUTORIAL and WE NEED INPUT FROM ALL OF YOU as CROWD-SCIENCE effort! 103d
Single nucleus RNASeq profiling of mouse lung: reduced dissociation bias and improved detection of rare cell types compared with single cell RNASeq
bioRxiv 122d 2 tweets
RATIONALE: Single cell RNA-sequencing (scRNASeq) has led to multiple recent advances in our understanding of lung biology and pathophysiology, but utility is limited by the need for fresh samples, loss of cell types due to death or inadequate...
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Holger Heyn Bechmarking #scRNAseq vs #snRNAseq in lung tissue. 1. Same number of genes and molecules when including intronic reads. 2. Less mitochondrial and housekeeping genes in snRNA. 3. Much more epithelial cells snRNA. 4. Much less immune cells in snRNA. 122d
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
Genome Biology 146d 2 tweets
Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single...
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Holger Heyn OUT NOW! Evaluating transcription factor and pathway analysis tools on #singlecell #scRNAseq data by lab. More than happy to see this published . Thanks for involving us! 145d
Long-range single-molecule mapping of chromatin accessibility in eukaryotes
Nature Methods 149d 6 tweets
SMAC-seq combines long-read sequencing with open chromatin methylation by DNA methyltransferases to enable mapping of nucleosome position and chromatin accessibility.
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Holger Heyn Very elegant method for long-range mapping of open chromatin sites at single molecule level, SMAC-seq by lab. 146d
Sampling artifacts in single-cell genomics cohort studies
bioRxiv 175d 2 tweets
Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid,...
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Holger Heyn NIGHTMARE AFTER XMAS! SORRY/HAPPY to present our benchmarking work on #singlecell sample preservation artifacts. We detected strong systematic biases related to sampling timing! MUST-READ for #scRNAseq and #scATACseq of #biobank and clinical cohorts. 175d
High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
PubMed Central (PMC) 185d 1 tweets
High-fidelity preservation strategies for primary tissues are in great demand in the single cell RNAseq community. A reliable method would greatly expand the scope of feasible multi-site collaborations and maximize the utilization of technical...
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Holger Heyn Cold storage: Seems to be a viable option for blood/organs up to 96 hours after sample extraction. Initially shows by the Quake lab for mouse kidney () and followed up by Kerstin Meyer for lung, spleen, and esophagus tissue (). 185d
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
Genome Biology 185d 2 tweets
The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection...
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Holger Heyn Cold storage: Seems to be a viable option for blood/organs up to 96 hours after sample extraction. Initially shows by the Quake lab for mouse kidney () and followed up by Kerstin Meyer for lung, spleen, and esophagus tissue (). 185d
Spatial mapping of cell types by integration of transcriptomics data
bioRxiv 204d 1 tweets
Spatial transcriptomics and single cell RNA-sequencing offer complementary insights into the transcriptional expression landscape. We here present a probabilistic method that integrates data from both techniques, leveraging their respective...
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Holger Heyn PIXEL deconvonvolution of Spatial Transcriptomics spots with matched #singlecell RNAseq data. 204d