drosophila embryos  (Spatial Transcriptomics Inc)

Journal: Genome Biology

Article Title: Unravelling the progression of the zebrafish primary body axis with reconstructed spatiotemporal transcriptomics

doi: 10.1186/s13059-025-03917-8

Figure Lengend Snippet: The implementation of Palette resulting in more specific gene expression patterns. a Schematic diagram illustrating the procedure used to assess the performance of Palette, using two adjacent slices from the Stereo-seq data of E14-16 Drosophila embryo. Slice S05 was converted into a pseudo bulk, and Palette was then applied to infer the spatial gene expression, with slice S04 serving as the ST reference. The expression patterns of Palette S04 were compared to the original expression patterns of slice S05 to evaluate the performance of Palette. The orange and purple layers outside the ST data represent the spatial data from slices S05 and S04, respectively. b Boxplots showing the numbers of molecules and genes in each spot before and after implementing Palette. The substantial increase in gene number is due to the supplementation from neighbouring spots, based on the assumption that neighbouring spots within the same cluster exhibit similar gene expression patterns. c Heatmap showing the expression correlation of marker genes for each cluster before and after implementing Palette. The colour bar represents the Pearson correlation coefficient with positive correlation in red and negative correlation in blue. d Spatial expression patterns of marker genes on the Drosophila Stereo-seq slices. Intensity of colour represents the expression levels of each marker gene. For each gene, the spatial patterns from slice S05 and Palette S04 are shown on the left, and the ISH images from BDGP database are shown on the right. The intensities of signals along the AP axis, which is represented by the black dashed lines in the images, are shown below. A, anterior; P, posterior; ARI, Adjusted Rand Index; RSME, Root Mean Square Error. e The clustering and annotation of the selected slice from the Stereo-seq data of 5.25 hpf zebrafish embryo. f Circle plot showing the expression correlation network between the serial bulk data of 6 hpf zebrafish embryo and the pseudo bulk of the Stereo-seq slice. Stroke weight indicates the strength of the Pearson correlation coefficient. g Palette inferring spatial expression patterns of 6 hpf zebrafish embryo bulk data on the 5.25 hpf zebrafish Stereo-seq slice. Since zebrafish embryos at 5.25 hpf and 6 hpf exhibited similar expression patterns, we used Palette to infer spatial gene expression from the 6 hpf zebrafish embryo bulk data using the 5.25 hpf ST data as a reference. Intensity of colour represents the gene expression levels. For each gene, the spatial patterns from the Stereo-seq S10 slice and the Palette-implemented S10 slice are shown on the left, and the correlated ISH images shown on the right are from ZFIN and published data [ , ]

Article Snippet: The published data used in this study can be accessed through the following links or accession number: (1) Stereo-seq data of Drosophila embryos ( https://db.cngb.org/stomics/flysta3d/download/ ); [ , ]; (2) Stereo-seq data of zebrafish embryos ( https://db.cngb.org/stomics/zesta/download/ ); [ , ]; (3) Serial bulk RNA-seq data of 6-hpf zebrafish embryos: “ GSE59873 ” [ , ]; (4) live imaging data of zebrafish embryos (idr0068 from https://idr.openmicroscopy.org ) [ , ]; (5) Spatial transcriptomics data of human PDAC: GEO accession: “ GSE111672 ” [ , ]; (6) Bulk RNA-seq data of human PDAC: GEO accession: “ GSE171485 ” [ , ]; (7) MERFISH data of mouse hypothalamus: GEO accession: “ GSE113576 ” [ , ]; (8) Bulk RNA-seq data of mouse hypothalamus region: GEO accession: “ GSE192999 ” [ , ]; (9) Visium data of melanoma tissues are available at https://www.spatialresearch.org/resources-published-datasets/doi-10-1158-0008-5472-can-18-0747/ [ ].

Techniques: Gene Expression, Expressing, Marker

Journal: Nature Communications

Article Title: A temperature-sensitive CRISPR-Cas12a system for sterile insect technique

doi: 10.1038/s41467-025-64685-4

Figure Lengend Snippet: a We targeted the following loci: (1) βtubulin ( βtub ) which is testis-specific and causes male sterility when mutated, was targeted by four gRNAs (g1–g4); (2) sex lethal ( sxl ), which causes female lethality when disrupted, was targeted by four gRNAs (g1–g4); (3) transformer ( tra ), where targeting the female-specific exon results in intersex individuals was targeted by two gRNAs; and (4) double sex ( dsx ), where targeting the female-specific transcript leads to intersex phenotypes was targeted by one gRNA. Boxes indicate the exons and specific female and male transcripts are shown in different colors. Red vertical lines indicate premature stop codons. b To generate transgenic insects, gRNA-expressing constructs were built with mini-white, CFP/GFP markers for selection and tracking, and tRNA-based gRNA expression under the Drosophila U6-3 promoter. Constructs were integrated into the genome using PhiC31-mediated recombination.

Article Snippet: We employed 60 × 15 mm grape plates that were ordered from Lab Express (Cat. # 7007-60), and Drosophila Embryo Collection Cages from Genesee Scientific (Cat. # 59-100).

Techniques: Sterility, Transgenic Assay, Expressing, Construct, Selection

Journal: Nature Communications

Article Title: A temperature-sensitive CRISPR-Cas12a system for sterile insect technique

doi: 10.1038/s41467-025-64685-4

Figure Lengend Snippet: a To generate transgenic insects, gRNA-expressing constructs were built with mini-white, CFP/GFP markers for selection and tracking, and tRNA-based gRNA expression under the Drosophila U6-3 promoter. Constructs were integrated into the genome using PhiC31-mediated recombination. b Females carrying Cas12a were crossed to homozygous males carrying gRNAs targeting the βtubulin gene (G0). G1 males carrying both transgenes were then single pair-crossed to wildtype females to evaluate male sterility. As shown in the G2 table, these experiments were performed at 18 °C ( n = 8) and at 29 °C ( n = 15). c Editing rates at the two different target sites are shown for the βtub gene at 18 °C and 29 °C. For both temperatures, target sites were evaluated using two biological replicates or independent samples, each replicate containing 10 flies. Data are presented as mean values +/− SD. d Cas12a females were crossed to heterozygous males carrying gRNAs targeting sex lethal gene (G0). Then, G1 progeny was analyzed after one generation (G1). As shown in the G1 tables, these experiments were performed at 18 °C ( n = 15) and at 29 °C ( n = 17); average percentages from all experiments are shown in each table for the genotypes observed. e Editing rates at the two different target sites are shown for the sxl gene at 18 °C and 29 °C. For both temperatures, target sites were evaluated using two biological replicates or independent samples, each replicate containing 10 flies. Data are presented as mean values +/− SD.

Article Snippet: We employed 60 × 15 mm grape plates that were ordered from Lab Express (Cat. # 7007-60), and Drosophila Embryo Collection Cages from Genesee Scientific (Cat. # 59-100).

Techniques: Transgenic Assay, Expressing, Construct, Selection, Sterility