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recombinant bcan  (R&D Systems)


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    Structured Review

    R&D Systems recombinant bcan
    ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 <t>(BCAN</t> + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .
    Recombinant Bcan, supplied by R&D Systems, used in various techniques. Bioz Stars score: 94/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/brevican/Recombinant+Mouse+Brevican+Protein%2C+CF/bio_rxiv__64898__2026__03__26__713760-254-27-31
    Average 94 stars, based on 2 article reviews
    recombinant bcan - by Bioz Stars, 2026-09
    94/100 stars

    Images

    1) Product Images from "Spike-in probe-enhanced single-cell RNA-seq reveals post-infusion transcriptomic remodeling of “prime-and-kill” synNotch-CAR-T cells"

    Article Title: Spike-in probe-enhanced single-cell RNA-seq reveals post-infusion transcriptomic remodeling of “prime-and-kill” synNotch-CAR-T cells

    Journal: bioRxiv

    doi: 10.64898/2026.03.26.713760

    ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 (BCAN + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .
    Figure Legend Snippet: ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 (BCAN + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .

    Techniques Used: In Vitro, In Vivo, Expressing, Derivative Assay, Co-Culture Assay, Flow Cytometry, Quantitative RT-PCR, RNA Sequencing, Gene Expression

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    Article Title: Deep Sequencing of Complex Proteoglycans: A Novel Strategy for High Coverage and Site-specific Identification of Glycosaminoglycan-linked Peptides
    Article Snippet: Bovine articular cartilage aggrecan, bovine articular cartilage decorin, chymotrypsin, endoproteinase Glu-C, dithiothreitol, iodoacetamide, sodium dodecyl sulfate, urea, MS-safe protease and phosphatase inhibitors, and chondroitinase ABC were purchased from Sigma-Aldrich (St. Louis, MO). .. Recombinant human neurocan and brevican were purchased from R&D systems. .. Recombinant human neurocan and brevican were purchased from R&D systems.

    Article Title: Analysis of complex proteoglycans using serial proteolysis and EThcD provides deep N- and O-glycoproteomic coverage.
    Article Snippet: Proteoglycans are a small but diverse family of proteins that play a wide variety of roles at the cell surface and in the extracellular matrix.. In addition to their glycosaminoglycan (GAG) chains, they are Nand O-glycosylated.. All of these types of glycosylation are crucial to their function but present a considerable analytical challenge.

    Cell Culture:

    Article Title: Astrocyte-derived factors regulate CNS myelination.
    Article Snippet: .. The inserts with the slices were cultured in a clear 6-well plate (Falcon 6-well Clear Flat Bottom 353,224) with 1.1 mL brain slice (BSC) medium (50% Minimum essential medium (Gibco 21,090-022), 25% Hank's Balanced Salt Solution (Gibco 14,175-053), 25% inactivated horse serum (VWR 97068-085), 25 mM HEPES (Gibco 15,630-056), 1 mM L-glutamine, 20 ng/mL insulin) with 0.01–0.2 μM brevican (R&D 4009-BC) or H2O control. .. BSC medium was replaced the next day and for the developmental study every other day renewed for 14 days followed by 4% paraformaldehyde (PFA) fixation for 30 min. P7 cerebellar slices were demyelinated 14 days post seeding using 0.5 mg/mL LPC in NaCl (Sigma L4129) for 16 h. Subsequently, the slices were treated with brevican (0.01– 0.2 μM R&D 4009-BC) or H2O for 14 days before the slices were 4% PFA-fixed and analyzed by immunohistochemistry.

    Slice Preparation:

    Article Title: Astrocyte-derived factors regulate CNS myelination.
    Article Snippet: .. The inserts with the slices were cultured in a clear 6-well plate (Falcon 6-well Clear Flat Bottom 353,224) with 1.1 mL brain slice (BSC) medium (50% Minimum essential medium (Gibco 21,090-022), 25% Hank's Balanced Salt Solution (Gibco 14,175-053), 25% inactivated horse serum (VWR 97068-085), 25 mM HEPES (Gibco 15,630-056), 1 mM L-glutamine, 20 ng/mL insulin) with 0.01–0.2 μM brevican (R&D 4009-BC) or H2O control. .. BSC medium was replaced the next day and for the developmental study every other day renewed for 14 days followed by 4% paraformaldehyde (PFA) fixation for 30 min. P7 cerebellar slices were demyelinated 14 days post seeding using 0.5 mg/mL LPC in NaCl (Sigma L4129) for 16 h. Subsequently, the slices were treated with brevican (0.01– 0.2 μM R&D 4009-BC) or H2O for 14 days before the slices were 4% PFA-fixed and analyzed by immunohistochemistry.

    Control:

    Article Title: Astrocyte-derived factors regulate CNS myelination.
    Article Snippet: .. The inserts with the slices were cultured in a clear 6-well plate (Falcon 6-well Clear Flat Bottom 353,224) with 1.1 mL brain slice (BSC) medium (50% Minimum essential medium (Gibco 21,090-022), 25% Hank's Balanced Salt Solution (Gibco 14,175-053), 25% inactivated horse serum (VWR 97068-085), 25 mM HEPES (Gibco 15,630-056), 1 mM L-glutamine, 20 ng/mL insulin) with 0.01–0.2 μM brevican (R&D 4009-BC) or H2O control. .. BSC medium was replaced the next day and for the developmental study every other day renewed for 14 days followed by 4% paraformaldehyde (PFA) fixation for 30 min. P7 cerebellar slices were demyelinated 14 days post seeding using 0.5 mg/mL LPC in NaCl (Sigma L4129) for 16 h. Subsequently, the slices were treated with brevican (0.01– 0.2 μM R&D 4009-BC) or H2O for 14 days before the slices were 4% PFA-fixed and analyzed by immunohistochemistry.

    Bioprocessing:

    Article Title: Ankyrin-R regulates fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K + channels
    Article Snippet: Activity for these tasks was recorded and analyzed using the ANY-maze Video Tracking System version 4.99v (Stoelting Co, Wood Dale, IL). .. The primary antibodies used here include: mouse monoclonal antibodies against AnkR (UC Davis/NIH NeuroMab Facility Cat# 75-380, RRID:AB_2491109), β 1 spectrin (UC Davis/NIH NeuroMab Facility Cat# 73-374, RRID:AB_2315814), AnkG (UC Davis/NIH NeuroMab Facility Cat# 73-146, RRID:AB_10697718), parvalbumin (UC Davis/NIH NeuroMab Facility Cat# 73-455, RRID:AB_2629420), actin (Millipore Cat# MAB1501, RRID:AB_2223041), tenascinR (R and D Systems Cat# MAB1624, RRID:AB_2207001), aggrecan (Millipore Cat# AB1031, RRID:AB_90460), brevican (UC Davis/NIH NeuroMab Facility Cat# 75-294, RRID:AB_2315824), NrCAM (R and D Systems Cat# MAB2034, RRID:AB_2267411), Kv3.1b (UC Davis/NIH NeuroMab Facility Cat# N16B/8, RRID:AB_2750730 and Thermo Fisher Cat# MA5-27684, RRID:AB_2735238), Kv3.3 (Antibodies-Online Cat# ABIN572016, RRID:AB_10782137), Kv7.2 (James Trimmer, University of California at Davis Cat# N26A/23, RRID:AB_2750761), Flag-tag or DDDDK-tag (MBL International Cat# M185-3L, RRID:AB_11123930); rabbit polyclonal antibodies against AnkR( ) (RRID:AB_2833096), Ank1 (Thermo Fisher Scientific Cat# PA5-63372, RRID:AB_2638015), neurofilament M (Millipore Cat# AB1987, RRID:AB_91201), parvalbumin (Novus Cat# NB120-11427, RRID:AB_791498), versican (Millipore Cat# AB1032, RRID:AB_11213831), PlexinA4 (Abcam Cat# ab39350, RRID:AB_944890), and neuropilin-1 (GeneTex Cat# GTX16786, RRID:AB_422398), Kv3.1b (Alomone Labs Cat# APC-014, RRID:AB_2040166), Kv3.3 (Alomone Labs Cat# APC-102, RRID:AB_2040170), GFP (Thermo Fisher Scientific, Cat# A-11122, RRID: AB_221569); and chicken polyclonal antibody against Neurofascin (R and D Systems Cat# AF3235, RRID:AB_10890736). .. Wisteria Floribunda lectins used were: Fluorescein labeled (Vector Laboratories Cat# FL-1351, RRID:AB_2336875 and Bioworld Cat# 21761065-1, RRID:AB_2833087), and Texas-Red (EY Laboratories Cat# F-3101-1, RRID:AB_2315605).

    Incubation:

    Article Title: Cleavage of proteoglycans, plasma proteins and the platelet-derived growth factor receptor in the hemorrhagic process induced by snake venom metalloproteinases
    Article Snippet: Skin proteins from control and HF3-treated animals (30 μg), PDGFR-α (recombinant mouse PDGFR-α-Fc chimera), and PDGFR-β (recombinant mouse PDGFR-β-Fc chimera) (10 ng) were submitted to SDS-PAGE (10% SDS–polyacrylamide gel) under reducing conditions and transferred onto nitrocellulose membranes (GE Healthcare) . .. Membranes were blocked for 3 h in PBS-T buffer (150 mM sodium chloride, 20 mM sodium phosphate, pH 7.1, and 0.1% Tween 20) containing 5% nonfat milk and were then incubated for 16 h, according to manufacturer’s instructions, with antibodies recognizing mouse lumican (AF2745; R&D Systems), mimecan (AF2949; R&D Systems), syndecan-1 (AF3190; R&D Systems), PDGFR-α (AF1062; R&D Systems), PDGFR-β (AF1042; R&D Systems) and MMP9 (ab38898; Abcam) or human aggrecan (AF1220; R&D Systems), brevican (AF4009, R&D Systems), biglycan (AF2667; R&D Systems), decorin (AF143; R&D Systems), and glypican (AF4519; R&D Systems). .. After incubation for 1 h with specific anti-IgG secondary antibodies (Sigma-Aldrich, Vector Laboratories or R&D systems), conjugated to peroxidase, immunoreactive signals were visualized by enhanced chemiluminescence using ECL prime Western Blotting detection reagent (GE Healthcare) and a chemiluminescence documentation system (Uvitec).

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    ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 <t>(BCAN</t> + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .
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    ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 <t>(BCAN</t> + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .
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    ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 <t>(BCAN</t> + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .
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    ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 <t>(BCAN</t> + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .
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    Image Search Results


    ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 (BCAN + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .

    Journal: bioRxiv

    Article Title: Spike-in probe-enhanced single-cell RNA-seq reveals post-infusion transcriptomic remodeling of “prime-and-kill” synNotch-CAR-T cells

    doi: 10.64898/2026.03.26.713760

    Figure Lengend Snippet: ( A–C ) Histograms and empirical cumulative distribution function (ECDF) plots showing distribution of maxUMI CAR values in in vitro E-SYNC cells ( A ), in vitro B-SYNC cells ( B ), and in vivo samples ( C ). In the histograms, the bin width is 1, and the Y-axis is shown on a log 10 scale. In both histograms and ECDF plots, maxUMI CAR values >50 were capped at 50 for visualization. (D) Dot plot showing expression of representative DEGs by sample type (same gene list as in and ), stratified by CAR-expressing versus non-expressing groups. (E) Swarm plot and ECDF plot depicting the distribution of TRM core gene signature scores. Differences between CAR-positive and -negative cells within the brain were assessed using the Kolmogorov–Smirnov test ( P = 4.0 × 10 -5 ). (F) ECDF plots comparing the nCount_RNA and nFeature_RNA values between CAR-expressing and non-expressing cells within the brain-derived CD8 + synNotch-positive population. Differences were assessed using the Kolmogorov–Smirnov test. (G) Schematic overview of the time-course co-culture experiment of B-SYNC cells with the human GBM cell line GBM6 (BCAN + /EphA2 + /IL13Rɑ2 + ). Co-culture was performed using 24-well plates, with each well containing 0.5 × 10 5 GBM cells and 1 × 10 6 CD8 + B-SYNC cells. The data presented are representative of two independent experiments using different donors. Additional data are shown in Fig. S16 . (H) Flow cytometry analysis showing the percentage of cells expressing GFP fused to CAR within the live, singlet, non-tumor (mCherry-negative) population. Corresponding scatter plots are shown in Fig. S16 . (I) RT-qPCR data showing CAR transcript abundance across conditions. Relative expression was calculated using the 2 -ΔΔCq method, with the B-SYNC no-stimulation (no-stim) condition and the RPS18 transcript as references. ( J–K ) Bulk RNA-seq principal component analysis (PCA) plot ( J ) and gene expression heatmap ( K ) illustrating transcriptomic similarities and differences across samples. The heatmap displays scaled expression of 6,885 genes expressed in the B-SYNC no-stim sample at transcripts-per-million (TPM) ≥ 10, sorted by the magnitude of expression changes between no-stim and post-stimulation conditions. ( L ) Representative genes minimally expressed without co-culture but upregulated and sustained after co-culture. The full list of gene expression comparisons is provided in Supplementary Table S13 .

    Article Snippet: To prepare the B-SYNC primed sample, 2 × 10 4 cells were cultured for 24 hours on wells coated with Laminin (100 μg/ml, Thermo Fisher Scientific,23017015) and recombinant BCAN (25 μg/ml; R&D Systems, 7188-BC-050 and 4009-BC-050).

    Techniques: In Vitro, In Vivo, Expressing, Derivative Assay, Co-Culture Assay, Flow Cytometry, Quantitative RT-PCR, RNA Sequencing, Gene Expression