Journal: Journal of Neurochemistry

Article Title: A High‐Resolution Transcriptomic Atlas of Cell Types in the Ventral Visual Thalamus

doi: 10.1111/jnc.70406

Figure Lengend Snippet: snRNA‐Seq identifies distinct neuronal and glial cell types in vLGN. (A) Schematic of viral infection following AAV1‐Cre injection. (B) Trans‐synaptic labeling of retinorecipient cells in ventral lateral geniculate nucleus (vLGN) of H2B‐transgenic mice following intraocular delivery of AAV1‐Cre. White dashed line outlines vLGN. mCherry(H2B)‐labeled cells are present in vLGN (arrowheads). (C) Identification and isolation of H2b‐mCherry+ nuclei by FACS sorting. (D) UMAP (uniform manifold approximation and projection) plot of 10 266 cell nuclei from the ventral lateral geniculate nucleus (vLGN), clustered by expression of high‐variance genes and colored according to cluster identity. (E) Violin plots showing expression of pan‐neuronal marker genes ( Syn1, Rbfox3 ); oligodendrocyte marker gene ( Olig1 ); macrophage marker gene ( Cx3cr1 ); endothelial cell marker gene ( Cldn5 ); pericyte marker gene ( Vtn ); astrocyte marker genes ( Aldoc ); microglia marker gene ( Mrc1 ); excitatory neuron marker gene ( Slc17a6, Slc17a7 ); and inhibitory neuron marker genes ( Gad1, Gad2 ). (F) UMAP recolored to illustrate expression levels of marker genes. (G) UMAP clustered by expression of high‐variance genes and colored according to predicted cell type.

Article Snippet: Resource availability : A user‐friendly interface for visualizing and exploring the snRNA‐Seq data is available at the Broad Institute Single Cell Portal at https://singlecell.broadinstitute.org/single_cell/study/SCP3575 .

Techniques: Infection, Injection, Labeling, Transgenic Assay, Isolation, Expressing, Marker

Journal: Journal of Neurochemistry

Article Title: A High‐Resolution Transcriptomic Atlas of Cell Types in the Ventral Visual Thalamus

doi: 10.1111/jnc.70406

Figure Lengend Snippet: snRNA‐Seq elucidates 13 retinorecipient neuronal types in vLGN. (A) UMAP (uniform manifold approximation and projection) of 4489 neuron cell nuclei from the ventral lateral geniculate nucleus, clustered by expression of high‐variance genes and colored according to cluster identity. (B) Neuronal UMAP recolored to illustrate expression of 89 mCherry+ vLGN nuclei following AAV injection in neurons. (C) Dot plot of neuronal clusters showing the expression of inhibitory marker genes ( Gad1 and Gad2 ) and excitatory marker genes ( Slc17a6 and Slc17a7 ) separated by original identity. (D) Dot plot of neuronal clusters showing the expression of Nxph1 (vLGNe) separated by original identity. (E) Neuron UMAP recolored to illustrate expression levels of Nxph1 .

Article Snippet: Resource availability : A user‐friendly interface for visualizing and exploring the snRNA‐Seq data is available at the Broad Institute Single Cell Portal at https://singlecell.broadinstitute.org/single_cell/study/SCP3575 .

Techniques: Expressing, Injection, Marker

Journal: BMC Genomics

Article Title: LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing

doi: 10.1186/s12864-020-07207-4

Figure Lengend Snippet: Candidate gene fusions detected by LongGF on long-read RNA-seq data for universal human reference mRNA sample and for a patient with AML. “A:B” denotes a gene fusion of gene A and gene B. The 6 known gene fusions for ‘UHR Nanopore’ rows are used for evaluating gene fusion detection, but additional gene fusions may be present for UHR samples

Article Snippet: To further evaluate the real-world utility of LongGF, we tested LongGF on several long-read RNA-seq data sets: Oxford Nanopore data (via direct mRNA sequencing) and PacBio data on the universal human reference RNA-seq sample, as well as Nanopore data (via full-length cDNA sequencing) of a patient with acute myeloid leukemia (AML).

Techniques:

Journal: BMC Genomics

Article Title: LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing

doi: 10.1186/s12864-020-07207-4

Figure Lengend Snippet: Examination of BCAS4-BCAS3 fusion in the Nanopore direct mRNA sequencing data on the UHR sample. a The IGV plot for the gene fusion at the genomic region around BCAS4. b The IGV plot for the gene fusion at the genomic region around BCAS3. The vertical dotted line indicates the genomic location where breakpoint occurs

Article Snippet: To further evaluate the real-world utility of LongGF, we tested LongGF on several long-read RNA-seq data sets: Oxford Nanopore data (via direct mRNA sequencing) and PacBio data on the universal human reference RNA-seq sample, as well as Nanopore data (via full-length cDNA sequencing) of a patient with acute myeloid leukemia (AML).

Techniques: Sequencing

Journal: BMC Genomics

Article Title: LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing

doi: 10.1186/s12864-020-07207-4

Figure Lengend Snippet: Examination of RUNX1T1-RUNX1 fusion in Nanopore long-read RNA-Seq data and Sanger sequencing data on a patient with AML. a The IGV plot for the gene fusion at the genomic region around RUNX1T1. b The IGV plot for the gene fusion at the genomic region around RUNX1. c the result from Sanger sequencing. The vertical dotted line indicates the genomic location where breakpoint occurs. The Sanger sequence in ( c ) is the complementary of the sequences in ( a ) and ( b )

Article Snippet: To further evaluate the real-world utility of LongGF, we tested LongGF on several long-read RNA-seq data sets: Oxford Nanopore data (via direct mRNA sequencing) and PacBio data on the universal human reference RNA-seq sample, as well as Nanopore data (via full-length cDNA sequencing) of a patient with acute myeloid leukemia (AML).

Techniques: RNA Sequencing, Sequencing

Journal: Biology

Article Title: Molecular and Functional Characterization of Neuropeptide F Receptor in Pomacea canaliculata : Roles in Feeding and Digestion and Communication with the Insulin Pathway

doi: 10.3390/biology14091241

Figure Lengend Snippet: Amino acid (aa) sequence alignments ( A ) and neighbor-joining phylogeny of PcNPFR ( B ) against orthologs from other species. Identical residues among receptors were shaded in black, while 80% and 60% conserved substitutions in pink and cyan, respectively. Horizontal bars denoted TM helix 1–7. Typical rhodopsin-like GPCR motifs were marked by red boxes. In the phylogenetic tree, dots at branch nodes represented bootstrap values (50%). A scale bar indicated that the average number of aa substitutions per site was 0.2. The D. melanogaster neuropeptide F receptor was chosen as the outgroup. The aligned NPFR/NPYR homologs were retrieved from the NCBI database under the following accession numbers: XP_025096430.1 [ Pomacea canaliculata ], XP_005089880.1 [ Aplysia californica ], XP_055874125.1 [ Biomphalaria glabrata ], XP_046372073.2 [ Haliotis rufescens ], XP_041369772.1 [ Gigantopelta aegis ], XP_050395368.1 [ Patella vulgata ], GFO06936.1 [ Plakobranchus ocellatus ], GFR99678.1 [ Elysia marginata ], XP_022289835.1 [ Crassostrea virginica ], XP_048746931.2 [ Ostrea edulis ], XP_052224883.1 [ Dreissena polymorpha ], XP_006509657.1 [ Mus musculus ], NP_524245.3 [ Drosophila melanogaster ], XP_054206094.1 [ Homo sapiens ].

Article Snippet: The amino acid (aa) sequence of PcNPFR (GenBank accession number, XP_025096430.1 ) were selected as the query to map the National Center for Biotechnology Information (NCBI) GenBank database via BlastP ( https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome accessed on 14 July 2025) and retrieve available NPFR orthologs from other species.

Techniques: Sequencing

Journal: Cellular and Molecular Immunology

Article Title: The innate immune effector ISG12a promotes cancer immunity by suppressing the canonical Wnt/β-catenin signaling pathway

doi: 10.1038/s41423-020-00549-9

Figure Lengend Snippet: ISG12a suppresses canonical Wnt/β-catenin signaling. a Enrichment analysis of 261 DEGs related to signal transduction pathways in Huh7 cells with ISG12a knockdown, as assayed by RNA sequencing. The log2(Fold Change) ≥ 1.00 and FDR ≤ 0.01 from three biological replicates. b Immunoblots showing levels of EMT-associated markers in Huh7 and HGC-27 cells with ISG12a knockdown. c Immunofluorescence staining for F-actin using phalloidin in Huh7 and HGC-27 cells with ISG12a knockdown. Nuclei were stained with DAPI. Scale bar, 10 μm. d Immunoblots showing levels of β-catenin and Axin in HLCZ01, LH86, Huh7, BGC-823, and HGC-27 cells. e Immunoblots showing levels of β-catenin and ISG12a in the cytoplasm and nucleus of Huh7 and HGC-27 cells with ISG12a knockdown. GAPDH and Lamin B1 served as loading controls for cytoplasmic and nuclear proteins, respectively. Cy Cytoplasm, Nu Nucleus. f Immunofluorescence staining for β-catenin in Huh7 and HGC-27 cells with ISG12a knockdown. Nuclei were stained with DAPI. Scale bar, 10 μm. g qRT-PCR analysis of ISG12a, c-Myc, and Cyclin D1 expression in Huh7 cells with ISG12a knockdown. h Fold change of luciferase expression of the TOP-Flash plasmid in Huh7 and HGC-27 cells with ISG12a knockdown. Experiments were independently repeated two (h) or three (b–g) times, with similar results. Two-tailed Student’s t tests were performed to analyze the data, and data are presented as means ± SD of three biological replicates. **p < 0.01 and ***p < 0.001

Article Snippet: RNA sequencing RNA sequencing of three independent biological replicates was conducted at BGI (Shenzhen, Guangzhou, China).

Techniques: Transduction, Knockdown, RNA Sequencing, Western Blot, Immunofluorescence, Staining, Quantitative RT-PCR, Expressing, Luciferase, Plasmid Preparation, Two Tailed Test

Journal: Cellular and Molecular Immunology

Article Title: The innate immune effector ISG12a promotes cancer immunity by suppressing the canonical Wnt/β-catenin signaling pathway

doi: 10.1038/s41423-020-00549-9

Figure Lengend Snippet: ISG12a induces the proteasomal degradation of β-catenin. a qRT-PCR analysis of expression of ISG12a, CTNNB1, Axin, CKIα, APC, and GSK3β mRNAs in Huh7 cells with ISG12a knockdown. b RNA sequencing showing the expression change of mRNAs associated with the canonical Wnt/β-catenin signaling pathway in Huh7 cells with ISG12a knockdown. The scale bar shows the expression change of genes by the log2(value+1) method. c–e Immunoblots showing β-catenin levels in Huh7 cells with ISG12a knockdown after treatment with 100 μg/ml CHX for different times (c) or 25 mM NH4Cl (d) or 25 μM MG132 (e) for 6 h. CHX cycloheximide. f Co-IP of ubiquitinated β-catenin (HA) in HEK293T cells overexpressing ISG12a. Cell lysates were immunoprecipitated with an anti-Flag antibody and examined for HA levels by immunoblotting. g Immunoblots showing levels of Flag, β-catenin, GSK3β, Axin, and Cyclin D1 in Huh7 cells after treatment with 25 μM MG132 for 6 h. ISG12a-silenced cancer cells were further transfected with p3×Flag-ISG12a or an empty vector for 48 h. Experiments were independently repeated two (c, d) or three (a, e–g) times, with similar results. Two-sided Student’s t tests were performed to analyze the results, and data are presented as means ± SD of three biological replicates. ***p < 0.001

Article Snippet: RNA sequencing RNA sequencing of three independent biological replicates was conducted at BGI (Shenzhen, Guangzhou, China).

Techniques: Quantitative RT-PCR, Expressing, Knockdown, RNA Sequencing, Western Blot, Co-Immunoprecipitation Assay, Immunoprecipitation, Transfection, Plasmid Preparation