Gene expression in Transcripts Per Kilobase Million (TPM) of desaturares, reductases and genes of the peripheral odorant reception repertoire with biased expression in the pheromone glands compared to antennae in the four New Zealand native leafroller moth species. Only genes showing a log fold ch...
Intra-tumour heterogeneity (ITH) presents a significant obstacle in formulating effective treatment strategies in clinical practice. Single-cell RNA sequencing (scRNA-seq) has evolved as a powerful instrument for probing ITH at the transcriptional level,
expression levels were converted to log2(TPMi,j/10 + 1), where TPMi,jrefers to the transcripts-per-million estimate for geneiin samplej. The TPM values were divided by 10 in every dataset to reflect an upper bound estimate of 100,000 for the number of transcripts in single-cell ...
1a). For 15 biopsies, we collected matching spatial data from serial sections of a second biopsy core from the same lesion/procedure, using up to four spatial methods and hematoxylin and eosin (H&E) staining (Fig. 1c, Extended Data Fig. 1a,b and Supplementary Tables 1 and 2)....
The discovery of TREM2 as a myeloid-specific Alzheimer’s disease (AD) risk gene has accelerated research into the role of microglia in AD. While TREM2 mouse models have provided critical insight, the normal and disease-associated functions of TREM2 in human microglia remain unclear. To examine...
To evaluate the influence of tissue-specific chromatin accessibility on gene expression, our first step was to identify tissue-restricted ATAC-seq peaks using DiffBind [37], with the following statistical cutoff: log2 Fold Change (L2FC) > 1 and FDR < 0.01. Among the 742,326 open chromatin ...
TPM (transcripts per kilobase per millions reads) or RPKM (reads per kilobase per millions reads). We denoteXi,jas the normalized expression level obtained from RPM values by further performing a log transformationXi,j = log(Ri,j + 0.1). For imputation, we examine one cell at a...
grapevine samples used to define the atlas. X-axis: number of miRNAs expressed in individual samples; Y-axis: different samples. Common refers to the number of miRNA expressed in all the samples. Total is the whole set of miRNAs expressed above the set threshold of 10 TPM in both ...
highly downregulated gene pair, MAL and AC103563.8, we used the pheatmap R package (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf) to perform unsupervised hierarchical clustering with normalised counts, which were log2 transformed after adding a constant (= 1) to all values. ...
(1,019 from CCLE plus 69 from HPA minus 33 common cell lines) for pathway analysis. Then, the read counts were normalized by DESeq2 (v1.34.0)55with respect to the size factor of each cell line and were further transformed by variance stabilizing transformation into log2space. To ...