Journal: Nature Biotechnology

Article Title: Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues

doi: 10.1038/s41587-021-01109-w

Figure Lengend Snippet: a , Workflow used to identify fCpG loci that exhibit high intraindividual heterogeneity. Input data were the ~850,000 CpG loci assayed by an Illumina EPIC array. We removed type I probes and probes that cross-hybridize highly homologous DNA regions. For each CpG locus, we calculated the standard deviation for each set of approximately four crypts per individual and then calculated the mean standard deviation across the cohort as a metric for the intraindividual heterogeneity. We selected the top 5% most highly variable CpG loci and then removed CpG loci that have a mean β value (across the entire cohort) less than 0.4 or greater than 0.6; kb, kilobases. b , Left: fCpGs are enriched for CpG loci not associated with any genes ( P = 6.5 × 10 −34 , chi-squared test). Right: the set of genes associated with fCpG loci exhibit lower average RNA expression ( P = 6.6 × 10 −6 , two-sided Welch’s t- test performed following the log-transformed data) in normal colon than those genes associated with non-fCpG loci (center line, median; box limits, upper and lower quartiles; whiskers, 1.5 interquartile range). *** P < 0.001. c , β values of fCpG loci are correlated between the bottom and top halves of a crypt.

Article Snippet: Illumina EPIC array data (colon, small intestine and endometrium) collected in the process of this study are currently available at the European Genome–Phenome Archive (EGA) (accession EGAS00001005514 ).

Techniques: Standard Deviation, RNA Expression, Transformation Assay

Journal: Genome Biology

Article Title: Linked optical and gene expression profiling of single cells at high-throughput

doi: 10.1186/s13059-020-01958-9

Figure Lengend Snippet: A high-throughput platform for linked optical phenotype and gene expression of single cells. a Monodisperse droplet emulsions containing encapsulated poly-T mRNA capture beads and cells are input into a microfluidic device. Fluorescence signal from droplets is interrogated and used to selectively dispense a cell and bead to indexed locations on a nanowell array. b Each bead binds mRNA from cell lysate as well as a unique combination of poly-A barcode oligos denoted by nanowell coordinate. c UMI counts on each bead are collected through sequencing into an expression matrix for each cell. Nanowell coordinate is assigned based on the abundance of barcode oligos and paired with fluorescence data obtained during cell sorting, which enables downstream linked analyses such as dimensionality reduction visualizations of gene expression paired with optical phenotype

Article Snippet: Barcoded mRNA capture beads are purchased through ChemGenes (MACOSKO-2011-10) and have a structure previously reported [ ].

Techniques: High Throughput Screening Assay, Expressing, Fluorescence, Sequencing, FACS

Journal: Cell

Article Title: Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity

doi: 10.1016/j.cell.2019.01.031

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Briefly, an array with ~90,000 nanowells is loaded with mRNA capture beads that are bound to oligos with a primer binding sequence, cell barcode (CB), unique molecular identifier (UMI) and polyT sequence (Chemgenes NC0927472).

Techniques: Recombinant, Hybridization, Luciferase, Transfection, Ligation, Sequencing, Mutagenesis, Clone Assay, Software