Luciano Martelotto 🛠🧬💻🇺🇸
Scientific Director Single Cell Core at Harvard Medical School | Research Associate in the Department of Systems Biology. Like/RT ≠ endorse
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Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing
Medical-epigenomics.org 135d 1 tweets
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Luciano Martelotto 🛠🧬💻🇺🇸 Finally available for the peeps! Scifi-Seq FULL protocol! Cleverly hacking @10xGenomics scRNA-Seq protocols to cost-effectively profile 100s of 1000s to millions of cells 135d
Single-cell multiomics: technologies and data analysis methods
Experimental & Molecular Medicine 144d 1 tweets
The expansion of single-cell profiling technologies will provide unprecedented insights into the molecular mechanisms inherent in disease. Novel technologies known collectively as ‘single-cell multiomics’ enable systematic, high-resolution profiling...
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Luciano Martelotto 🛠🧬💻🇺🇸 REVIEW 📢 A few very recent tech missing (SHARE-Seq, ASAP-Seq, etc) but still very comprehensive 🤙 Single-cell multiomics: technologies and data analysis methods 144d
Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions
Genome Medicine 155d 3 tweets
Solid tumors such as pancreatic ductal adenocarcinoma (PDAC) comprise not just tumor cells but also a microenvironment with which the tumor cells constantly interact. Detailed characterization of the cellular composition of the tumor...
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Luciano Martelotto 🛠🧬💻🇺🇸 Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions 155d
A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data
Nature Communications 187d 2 tweets
How cell clusters are defined in single-cell sequencing data has important consequences for downstream analyses and the interpretation of results, but is often not straightforward. Here, the authors present a new approach that enables the prediction...
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Luciano Martelotto 🛠🧬💻🇺🇸 #singleCellHeystack "A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data" 187d
Protein velocity and acceleration from single-cell multiomics experiments
Genome Biology 380d 3 tweets
The simultaneous quantification of protein and RNA makes possible the inference of past, present, and future cell states from single experimental snapshots. To enable such temporal analysis from multimodal single-cell experiments, we introduce an...
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Luciano Martelotto 🛠🧬💻🇺🇸 Protein velocity and acceleration from single-cell multiomics experiments 212d
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
Sciencedirect.com 243d 1 tweets
Most genetic variations associated with human complex traits are located in non-coding genomic regions. Therefore, understanding the genotype-to-pheno…
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Luciano Martelotto 🛠🧬💻🇺🇸 Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation 243d
A single-cell landscape of high-grade serous ovarian cancer
Nature Medicine 255d 4 tweets
Single-cell transcriptomics analysis of malignant ascites samples from patients with high-grade serous ovarian cancer reveals inter- and intra-patient heterogeneity in malignant cells, cancer-associated fibroblasts and macrophages.
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Luciano Martelotto 🛠🧬💻🇺🇸 A single-cell landscape of high-grade serous ovarian cancer 255d
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Genome Biology 274d 2 tweets
Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells...
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Luciano Martelotto 🛠🧬💻🇺🇸 A MUST READ piece on solid tissue dissociation for #scRNASeq. There are only two very well thought out papers on this topic out there and this is one of them...thanks to the authors! et al. 274d
Targeted Perturb-seq enables genome-scale genetic screens in single cells
Nature Methods 276d 5 tweets
Targeted sequencing of perturbation effects offers a sensitive approach to capture genes of interest in CRISPR-mediated screens, enabling genome-scale screens at higher scale and lower cost than whole-transcriptome Perturb-seq.
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Luciano Martelotto 🛠🧬💻🇺🇸 Targeted Perturb-seq enables genome-scale genetic screens in single cells 276d
ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
bioRxiv 279d 3 tweets
Single-cell sequencing technologies are revolutionizing biology, but are limited by the need to dissociate fresh samples that can only be fixed at later stages. We present ACME (ACetic-MEthanol) dissociation, a cell dissociation approach that fixes...
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Luciano Martelotto 🛠🧬💻🇺🇸 ACME (ACetic-MEthanol), fixes cells as they are being dissociated --> cells have high RNA integrity, can be cryopreserved multiple times, sorted by FACS and are permeable, enabling sci approaches. 279d
Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis
Communications Biology 301d 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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Luciano Martelotto 🛠🧬💻🇺🇸 Quantum Barcoding (QBC)! Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis | Communications Biology 301d
High throughput, error corrected Nanopore single cell transcriptome sequencing
bioRxiv 484d 6 tweets
Droplet-based high throughput single cell isolation techniques tremendously boosted the throughput of single cell transcriptome profiling experiments. However, those approaches only allow analysis of one extremity of the transcript after short read...
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Luciano Martelotto 🛠🧬💻🇺🇸 High throughput, error corrected #Nanopore single cell transcriptome sequencing | ⁦⁦⁩ ⁩ ⁦@10xGenomics⁩ 305d
A package to download free Springer books during Covid-19 quarantine
Stats and R 312d 3 tweets
This article presents a R package which allows to download free data science books in PDF that are made available by Springer during the COVID-19 quarantine
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Luciano Martelotto 🛠🧬💻🇺🇸 A package to download free Springer books during Covid-19 quarantine - Stats and R 307d
Decontamination of ambient RNA in single-cell RNA-seq with DecontX
Genome Biology 312d 1 tweets
Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s native mRNA and result in...
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Luciano Martelotto 🛠🧬💻🇺🇸 Issues with “the soup”? | Decontamination of ambient RNA in single-cell RNA-seq with DecontX | Genome Biology | Full Text 312d
Multi-Seq: my notes from the lab
protocols.io 317d 1 tweets
A1Please note these are just my notes and by no means are ground truth of how Multi-seq needs to be performed. I WELCOME to comments, suggestions and amendments.
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Luciano Martelotto 🛠🧬💻🇺🇸 Multi-Seq: my notes from the lab (latest version) 317d
Profiling the epigenome at home
bioRxiv 321d 7 tweets
We recently described CUT&Tag, a general strategy for epigenomic profiing in which antibody-tethered Tn5 transposase integrates DNA sequencing adapters at sites of specific chromatin protein binding or histone modification in intact cells or nuclei....
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Luciano Martelotto 🛠🧬💻🇺🇸 I admit....at first I was like “yeah, right”. But see for yourselves what the Henikoffs managed to pull off...LEGENDS! 👏. Kudos to them! Profiling the epigenome at home | doi: Also on 321d
protocols.io - Life Sciences Protocol Repository
Protocols.io 1376d 241 tweets
Open access repository of science methods and collaborative research platform. Discover corrections and optimizations of the protocols you use.
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Luciano Martelotto 🛠🧬💻🇺🇸 I admit....at first I was like “yeah, right”. But see for yourselves what the Henikoffs managed to pull off...LEGENDS! 👏. Kudos to them! Profiling the epigenome at home | doi: Also on 321d
CUT&[email protected]
protocols.io 321d 3 tweets
CUT&[email protected] uses a modification of Bench-top CUT&Tag which includes incubation in 0.1% SDS post-tagmentation for quantitative release of targeted fragments, followed directly...
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Luciano Martelotto 🛠🧬💻🇺🇸 I admit....at first I was like “yeah, right”. But see for yourselves what the Henikoffs managed to pull off...LEGENDS! 👏. Kudos to them! Profiling the epigenome at home | doi: Also on 321d
Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection
bioRxiv 323d 3 tweets
Respiratory failure is the leading cause of COVID-19 death and disproportionately impacts adults more than children. Here, we present a large-scale snATAC-seq dataset (90,980 nuclei) of the human lung, generated in parallel with snRNA-seq (46,500...
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Luciano Martelotto 🛠🧬💻🇺🇸 Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection | bioRxiv #snRNAseq #snATACseq 321d
Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
Genome Biology 1086d 2 tweets
High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell...
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Luciano Martelotto 🛠🧬💻🇺🇸 A revisit: Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads | Genome Biology | Full Text 321d