Shuoshuo Wang
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View article: Tumor-myeloid crosstalk drives therapy resistance in localized bladder cancer
Tumor-myeloid crosstalk drives therapy resistance in localized bladder cancer Open
Neoadjuvant cisplatin-based chemotherapy results in pathologic complete response for only a minority of patients with muscle-invasive bladder cancer (MIBC), and mechanisms of resistance and the effects of chemotherapy on the MIBC microenvi…
View article: Vaccine-educated T cells and a CD123 bispecific T-cell engager for treatment of acute myeloid leukemia
Vaccine-educated T cells and a CD123 bispecific T-cell engager for treatment of acute myeloid leukemia Open
T-cell engager (TCE) therapy has demonstrated significant therapeutic efficacy in patients with hematologic malignancies. Durable responses have been linked with T-cell clonotypic expansion. We hypothesized that combining vaccine-educated …
View article: The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers
The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers Open
Background Transcriptome sequencing (RNA-seq) is a powerful technology for gene expression profiling. Selection of optimal parameters for cDNA library generation is crucial for acquisition of high-quality data. In this study, we investigat…
View article: Preparation of Mouse Kidney for Spatial and Single-Cell Transcriptomics v1
Preparation of Mouse Kidney for Spatial and Single-Cell Transcriptomics v1 Open
This protocol describes the preparation of murine kidney specimens for single-cell and spatial transcriptomics through a non-survival procedure. The protocol can also be adapted for immunohistochemistry, immunofluorescence, or other molecu…
View article: Assessing RNA Integrity from FFPE samples for NGS, Single-Cell, Spatial Transcriptomics, and Molecular Pathology v1
Assessing RNA Integrity from FFPE samples for NGS, Single-Cell, Spatial Transcriptomics, and Molecular Pathology v1 Open
RNA quality in FFPE samples is highly variable, influenced by factors such as fixation protocols, tissue type, storage conditions, and necrosis. Formalin fixation exacerbates RNA degradation, resulting in fragmented molecules that pose cha…
View article: FixNCut v2.0Enhanced Cell and Tissue Fixation for Single Cell Assays v1
FixNCut v2.0Enhanced Cell and Tissue Fixation for Single Cell Assays v1 Open
The original FixNCut 1.0 protocol faced challenges in scalability bottlenecks due to the limited solubility and stability of DSP (dithiobis-succinimidyl propionate) NHS-esters in aqueous environments. Additionally, preparing the working so…
View article: Uncovering the Tumor Antigen Landscape in Patients Undergoing Dendritic Cell/Myeloma Fusion Vaccine with Lenalidomide Maintenance Treatment
Uncovering the Tumor Antigen Landscape in Patients Undergoing Dendritic Cell/Myeloma Fusion Vaccine with Lenalidomide Maintenance Treatment Open
Backgroun d: Identifying novel antigenic targets for immune-based therapy in Multiple Myeloma (MM) is a critical area of investigation. The BMT CTN 1401 (NCT02728102), a national randomized trial evaluating dendritic cell (DC)/MM fusion ce…
View article: BIDMC-TMC Nuclei Isolation from Frozen Cervix for Single Cell RNA-Seq v1
BIDMC-TMC Nuclei Isolation from Frozen Cervix for Single Cell RNA-Seq v1 Open
As a fibromuscular organ, human cervix samples are naturally resilient to withstand strains and deformation during pregnancy and birth. Due to its consistency and composition, dissociation and disrupting the cervix or other parts of uterus…
View article: The <scp>RNA</scp>‐binding protein <scp>RBMS3</scp> inhibits the progression of colon cancer by regulating the stability of <scp>LIMS1 mRNA</scp>
The <span>RNA</span>‐binding protein <span>RBMS3</span> inhibits the progression of colon cancer by regulating the stability of <span>LIMS1 mRNA</span> Open
Background The RNA‐binding motif single‐stranded interacting protein 3 (RBMS3) is a constituent of the RNA‐binding motif (RBM) protein family, which assumes a pivotal role in governing cellular biogenesis processes such as the cell cycle a…
View article: FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays
FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays Open
The quality of standard single-cell experiments often depends on the immediate processing of cells or tissues post-harvest to preserve fragile and vulnerable cell populations, unless the samples are adequately fixed and stored. Despite the…
View article: Genome-wide identification of the <i>OMT</i> gene family in <i>Cucumis melo</i> L. and expression analysis under abiotic and biotic stress
Genome-wide identification of the <i>OMT</i> gene family in <i>Cucumis melo</i> L. and expression analysis under abiotic and biotic stress Open
Background O-methyltransferase (OMT)-mediated O-methylation is a frequent modification that occurs during natural product biosynthesis, and it increases the diversity and stability of secondary metabolites. However, detailed genome-wide id…
View article: The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers
The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers Open
RNA sequencing (RNA-seq) is a powerful technology for gene expression and functional genomics profiling. Expression profiles generated using this approach can be impacted by the methods utilised for cDNA library generation. Selection of th…
View article: Additional file 3 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Additional file 3 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice Open
Additional file 3: Table S2. Differentially transcribed/translated genes under salt stress in seedling shoots of ‘Nipponbare’ (NB).
View article: Additional file 7 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Additional file 7 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice Open
Additional file 7: Table S6. Comparison of codon appearance at ribosome stalling sites with their corresponding frequency in gene coding sequences in ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86).
View article: Additional file 6 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Additional file 6 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice Open
Additional file 6: Table S5. Complete lists of gene ontology (GO) terms for genes translationally up- and down-regulated under salt stress in ‘Nipponbare’ (NB) or ‘Sea Rice 86’ (SR86).
View article: Additional file 5 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Additional file 5 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice Open
Additional file 5: Table S4. Differentially translated genes under salt stress in seedling shoots of ‘Nipponbare’ (NB) or ‘Sea Rice 86’ (SR86).
View article: Additional file 1 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Additional file 1 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice Open
Additional file 1: Table S1. Raw data of rice RNA-seq and ribo-seq libraries.
View article: Additional file 4 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Additional file 4 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice Open
Additional file 4: Table S3. Differentially transcribed/translated genes under salt stress in seedling shoots of ‘Sea Rice 86’ (SR86).
View article: The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity
The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity Open
Adhesion is essential for many marine sessile organisms. Unraveling the compositions and assembly of marine bioadheisves is the fundamental to understand their physiological roles. Despite the remarkable diversity of animal bioadhesion, ou…
View article: Ma2/d promotes myonuclear positioning and association with the sarcoplasmic reticulum
Ma2/d promotes myonuclear positioning and association with the sarcoplasmic reticulum Open
The cytoplasm of striated myofibers contains a large number of membrane organelles, including sarcoplasmic reticulum (SR), T-tubules and the nuclear membrane. These organelles maintain a characteristic juxtaposition that appears to be esse…
View article: Mechanotransduction via the LINC complex regulates DNA replication in myonuclei
Mechanotransduction via the LINC complex regulates DNA replication in myonuclei Open
Nuclear mechanotransduction has been implicated in the control of chromatin organization; however, its impact on functional contractile myofibers is unclear. We found that deleting components of the linker of nucleoskeleton and cytoskeleto…