Tag: DROP-seq

In GEO NCBI repository are available single cell data on PC9 untreated lung cancer cell line done in two different labs, using both 10XGenomics and Drop-seq platforms and produced from in vitro culture or xenograph experiments. set1: GSM3972657 PC9 in vitro dropseq Chicago (2500 cells) set2: SM4494347 PC9 in vitro…

Plants can be infected by diverse pathogenic organisms that modulate host cells to enable their growth and dissemination. Pathogens deploy a variety of manipulation strategies that can vary during the course of infection. These strategies include plant defense suppression as well as deployment of toxins and degradative enzymes to facilitate…

Subset specific clusters from drop-seq data, merge them and produce geneXcount expression matrix (bulk-seq format). 0 I have been following the R script in the link below: github.com/jeremymsimon/MouseCortex/blob/master/E14_processing.R My goal is to isolate only the radial glia clusters (which would be clusters 8, 10, 14 and 21), sum the expression…

hiPSC cell culture and differentiation hiPSCs were maintained on 1:40 matrigel (Corning, #354277) coated dishes in supplemented mTeSR-1 medium (StemCell Technologies, #85850) with 500 U ml−1 penicillin and 500 mg ml−1 streptomycin (Gibco, #15140122). For the differentiation of cortical neurons the protocol described previously21 was followed with slight modifications. Briefly, hiPSC colonies were seeded…

The Human Cell Atlas. New techniques in anatomical isolation and sequencing (e.g., single cell drop-seq) have, for example, defined 39 previously unknown functional cell types in the retina and 6 new dendritic cell families in the blood. The control of human physiology can be distilled into three sets of sensing/control…

Abstract Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating…

Fibroblast identification through single-cell RNA-sequencing analysis of whole-tissue homogenates derived from human NSCLC tumor samples. a Schematic illustrating sample processing and analysis methodology used to generate the target lung drop-seq (TLDS) dataset, comprised of human control (n = 6) and NSCLC (n = 12) samples. The Figure was partly generated using Servier Medical Art,…

doi: 10.1007/978-1-0716-2752-5_8. Affiliations Expand Affiliations 1 Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA, USA. ben.babcock@emory.edu. 2 Department of Neurology, University of North Carolina Medical School, Chapel Hill, NC, USA. Item in Clipboard Benjamin Babcock et al. Methods Mol Biol. 2023….

Baylor College of Medicine researchers in the Tolias Lab and the Xiaolong Jiang Lab are part of a global collaborative led by the Allen Institute to map the whole human brain. In what is being called the brain equivalent of the Human Genome Project, this initiative will map 200 billion cells in the human brain by…

This story has been updated to correct information about methods developed by Hao Wu.  NEW YORK – A new method for single-cell RNA sequencing may provide a triple threat: high sensitivity, full-length coverage of RNA, and high throughput. The researchers behind the method — dubbed “vast transcriptome analysis of single cells…

Filter Mus musculus TSV Brian P. Hermann GSE109033 10x Genonics Drop-seq single-cell RNA-seq of isolated Adult ID4-EGFP mouse spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells Expression profiling by high throughput sequencing Mus musculus 8 MTX TSV SRA Run Selector Brian P. Hermann Nov 06, 2018 GSE109037 10x Genomics Drop-seq single-cell…

Reviewer #1 (Public Review): Droplet-based single-cell method development has stalled in the past years. The field has been overtaken by commercial solutions that optimized performance, but at much higher costs and without any possibility for customization. More recently, combinatorial indexing methods (e.g. SPLIT-seq) have gained popularity, requiring no specialized equipment…

NEW YORK – Paris-based Scipio Bioscience this week announced the European launch of its Asteria hydrogel-based single-cell RNA-seq kit. With less reliance on equipment and reagents, the RNA-seq library preparation kit provides researchers with a flexible benchtop protocol for labeling, isolating, and lysing cells, and recovering labeled mRNA. The Asteria kit comes…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sun, 16 Jan 2022 16:45:58 +0100 Source: drop-seq Architecture: source Version: 2.5.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Andreas Tille <ti…@debian.org> Changes: drop-seq (2.5.1+dfsg-1) unstable; urgency=medium . * New upstream version * Add missing build dependency…

CROP-seq data analysis 1 Hi, I am a new bie to single cell sequencing analysis. I have to analyze CROP-seq data, I am going through the following paper, www.nature.com/articles/nmeth.4177. I have to use cell ranger ( instead of DROP-seq software) as the first step to process single cell data.I wanted…