Journal: Cell Reports Medicine

Article Title: Methionine intervention induces PD-L1 expression to enhance the immune checkpoint therapy response in MTAP-deleted osteosarcoma

doi: 10.1016/j.xcrm.2025.101977

Figure Lengend Snippet:

Article Snippet: SeekOne DD Single Cell 3′ Transcriptome kit , SeekGene , N/A.

Techniques: Control, Recombinant, Saline, Red Blood Cell Lysis, Lysis, Staining, Screening Assay, Transfection, Plasmid Preparation, In Vitro, CCK-8 Assay, Cell Isolation, Gene Expression, Sequencing, Methylation, In Vivo, Software, Microscopy, Refractive Index, Mass Spectrometry

Journal: Advanced Science

Article Title: Discovery and Application of Postnatal Nucleus Pulposus Progenitors Essential for Intervertebral Disc Homeostasis and Degeneration

doi: 10.1002/advs.202104888

Figure Lengend Snippet: Single‐cell RNA sequencing analysis of murine NP cells from Shh‐Cre;R26R tdTomato mice. A) Representative images of lumbar sections from 4‐week‐old Shh‐Cre;R26R tdTomato mice. The yellow circle shows NP tissue. Scale bars, 100 µm. B) Representative image of lumbar sections from 4‐week‐old Shh‐Cre; R26R confetti mice. Scale bars, 100 µm. C) Schematic workflow of the experimental strategy. Purified NP cells were isolated from Shh‐Cre;R26R tdTomato mice, enzymatically digested, and FACS‐sorted to isolate tdTomato + cells, which then underwent single‐cell RNA sequencing analysis via BD Rhapsody. D) qRT‐PCR of expression of NP marker genes, including Krt8 , Krt19 , T , Car3 , and CD24 related to HPRT in Shh‐Cre;R26R tdTomato+ and Shh‐Cre;R26R tdTomato‐ cells. E) Dot plots showing the expression of Col2a1 and Acan within the t‐SNE map. F,G) t‐SNE plots of glycolysis gene (F) and growth factor gene (G) distribution. H) Representative image of t‐SNE analysis showing the four clusters of Shh‐Cre;Ai9 + NP cells. (I) Relative percentage of each cluster among Shh‐Cre;Ai9 NP cells. J) Heatmap revealing the scaled expression of differentially expressed genes for each cluster. n = 3. Data are presented as mean ± standard deviation. * P < 0.05, ** P < 0.01; N.S., not significant as determined by two‐tailed Student t tests.

Article Snippet: Whole‐transcriptome libraries were prepared using the BD Rhapsody single‐cell whole‐transcriptome amplification (WTA) workflow, including random priming and extension (RPE), RPE amplification PCR, and WTA index PCR.

Techniques: RNA Sequencing Assay, Purification, Isolation, Quantitative RT-PCR, Expressing, Marker, Standard Deviation, Two Tailed Test

Journal: bioRxiv

Article Title: Neogenin-1 distinguishes between myeloid-biased and balanced Hoxb5 + mouse long-term hematopoietic stem cells

doi: 10.1101/608398

Figure Lengend Snippet: ( A ) Experimental design for bulk RNA-sequencing of NEO1 + and NEO1 − Hoxb5 + LT-HSCs. ( B ) Heatmap of differentially expressed genes ( n = 1,036 genes; FDR < 0.1) after pairwise comparison of NEO1 + ( n = 5 samples) and NEO1 − ( n = 5 samples) Hoxb5 + LT-HSC transcriptomes using DESeq2. Select genes are highlighted. Genes are ordered from left to right by log 2 fold enrichment in NEO1 + over NEO1 − Hoxb5 + LT-HSCs. ( C and D ) Gene set enrichment analysis (GSEA) plots of molecular signatures significantly enriched ( Q value < 0.05) over a gene list ordered by log 2 fold change, including ( C ) ‘G2_M_HALLMARK’ ( top ), ‘RIBOSOME_KEGG’ ( bottom ), ( D ) Myeloid LT-HSC signature ( top ), and non-myeloid LT-HSC signature ( bottom ) from Mann et al., 2018 . NES, normalized enrichment score. ( E to G ) Barplots showing log 2 and DESeq2-normalized gene expression for select genes associated with ( E ) granulocyte or monocyte, ( F ) platelet, or ( G ) stem programs. Statistical significance was calculated using a paired, two-tailed Student’s t -test adjusted for multiple hypothesis testing with Benjamini-Hochberg procedure. * P-adjusted < 0.05, ** P-adjusted < 0.01, *** P-adjusted < 0.001, **** P-adjusted < 0.0001. All barplots in this figure indicate mean ± SEM.

Article Snippet: Single cell transcriptomes of hematopoietic stem and progenitors (HSPCs) were acquired from GEO accessions, GSE90742, and from the Single-Cell Gene Expression Atlas for hematopoietic cells ( http://blood.stemcells.cam.ac.uk/single_cell_atlas.html ).

Techniques: RNA Sequencing, Comparison, Gene Expression, Two Tailed Test