Journal: Horticulture Research

Article Title: Transcriptional dynamics of the developing sweet cherry ( Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes

doi: 10.1038/hortres.2014.11

Figure Lengend Snippet: Summary of all contigs. Contigs were assembled de novo from Illumina sequenced cDNA fragments generated from sweet cherry ‘Regina’ fruit sampled at different developmental stages. Group 1 and 3 were termed ‘high abundance’ and Group 2 ‘low abundance’ contigs, based on the number of mapped reads per contig; threshold 30 mapped reads per sample or 75 reads total in all 24 samples. Group 3 consists of contigs with BLASTn hits ( e -value <1× −100 ) to bacterial, viral, rRNA or other sources as described in the section on ‘Materials and methods’

Article Snippet: Directional complementary DNA (cDNA) libraries were prepared at the GenXPro GmbH (Frankfurt am Main, Germany).

Techniques: Generated

Journal: Nature Communications

Article Title: Mapping recurrent mosaic copy number variation in human neurons

doi: 10.1038/s41467-024-48392-0

Figure Lengend Snippet: Overview of SCOVAL. A Single nuclei and bulk dural fibroblast DNA were analyzed using 10X platforms. (Images from vecteezy.com) B Single nuclei library quality is assessed based on median absolute deviation (MAD) and copy number thresholds are established using population statistics. Graphs depict schematized data; vertical red lines illustrate threshold strategy. C Candidate CNVs are identified based on altered read depth across consecutive genomic bins. D Heterozygous SNPs are phased using bulk linked-reads in chromosomal segments (“hap 1” or “hap 2”). E Absolute log2 ratios derived from “hap 1”/“hap 2” are calculated across ~100 SNP windows (see text). A deletion with concordant loss of heterozygosity (log2 ratio <> 0) is illustrated. F A highly aberrant CNV neuron (#5) shows representative Gingko calls (blue bars), duplications (e.g., green arrow), heterozygous deletions (e.g., black arrow), and homozygous deletions (e.g., orange arrow) and qualitatively concordant increases in absolute log2 ratio (white

Article Snippet: Using NeuN-positive nuclei (Supplementary Fig. ), two DNA libraries were prepared in separate lanes on the 10X Genomics Chromium platform (Fig. ); each lane produced ~1000 single neuronal genomic libraries with unique barcodes.

Techniques: Derivative Assay