evercode whole transcriptome wt kit (Parse Biosciences)

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Parse Biosciences evercode whole transcriptome wt kit

( A ) Schematic depicting the computational workflow for constructing the fetal whole-brain single-cell atlas and fetal midbrain subatlas, followed by their downstream applications. This includes projecting in vitro–derived datasets onto these reference atlases to evaluate their transcriptional fidelity. Created in BioRender. Toh, H. (2025); https://BioRender.com/pl47oha . ( B ) Dotplot of gene expression of known marker genes across different annotated cell types in the fetal whole-brain atlas. Uniform Manifold Approximation and Projection (UMAP) plot of fetal whole-brain atlas showing ( C ) the annotated cell types, ( D ) the single-cell study, ( E ) the embryonic age in postconception week, and ( F ) the gene expression of known marker genes for selected cell types. ( G ) Schematic depicting the determination of region specificity by comparing the region identity of each cell’s k -nearest neighbors. Created in BioRender. Toh, H. (2025); https://BioRender.com/pl47oha . ( H ) Heatmap showing the average proportion of k -nearest neighbors mapping to the corresponding brain region (midbrain, forebrain, or hindbrain) across different cell types. UMAP plot of dopaminergic (DA) neurons showing ( I ) the brain region identity, the midbrain region <t>gene</t> <t>expression</t> <t>signature,</t> the forebrain region gene expression signature, and the hindbrain region gene expression signature. ( J ) Heatmap of gene expression of top 10 marker genes, ordered by log2 fold change, for each brain region in DA neurons.

Evercode Whole Transcriptome Wt Kit, supplied by Parse Biosciences, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/evercode+cell+fixation+v2+kit/kit+transcriptome+whole/pmc12577693-241-8-6
Average 86 stars, based on 1 article reviews

evercode whole transcriptome wt kit - by Bioz Stars, 2026-09

86/100 stars

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1) Product Images from "BrainSTEM: A single-cell multiresolution fetal brain atlas reveals transcriptomic fidelity of human midbrain cultures"

Article Title: BrainSTEM: A single-cell multiresolution fetal brain atlas reveals transcriptomic fidelity of human midbrain cultures

Journal: Science Advances

doi: 10.1126/sciadv.adu7944

Figure Legend Snippet: ( A ) Schematic depicting the computational workflow for constructing the fetal whole-brain single-cell atlas and fetal midbrain subatlas, followed by their downstream applications. This includes projecting in vitro–derived datasets onto these reference atlases to evaluate their transcriptional fidelity. Created in BioRender. Toh, H. (2025); https://BioRender.com/pl47oha . ( B ) Dotplot of gene expression of known marker genes across different annotated cell types in the fetal whole-brain atlas. Uniform Manifold Approximation and Projection (UMAP) plot of fetal whole-brain atlas showing ( C ) the annotated cell types, ( D ) the single-cell study, ( E ) the embryonic age in postconception week, and ( F ) the gene expression of known marker genes for selected cell types. ( G ) Schematic depicting the determination of region specificity by comparing the region identity of each cell’s k -nearest neighbors. Created in BioRender. Toh, H. (2025); https://BioRender.com/pl47oha . ( H ) Heatmap showing the average proportion of k -nearest neighbors mapping to the corresponding brain region (midbrain, forebrain, or hindbrain) across different cell types. UMAP plot of dopaminergic (DA) neurons showing ( I ) the brain region identity, the midbrain region gene expression signature, the forebrain region gene expression signature, and the hindbrain region gene expression signature. ( J ) Heatmap of gene expression of top 10 marker genes, ordered by log2 fold change, for each brain region in DA neurons.

Techniques Used: In Vitro, Derivative Assay, Gene Expression, Marker

( A ) Schematic depicting the BrainSTEM framework’s two-tier mapping process of query datasets onto our fetal whole-brain atlas and midbrain subatlas. Created in BioRender. Toh, H. (2025); https://BioRender.com/pl47oha . Proportion plots of in vivo brain tissue single-cell studies across different developmental stages showing ( B ) proportion of cells confidently assigned, ( C ) region.lineage proportions for confidently assigned cells, and ( D ) cell-type proportions for confidently assigned cells. ( E ) Cell-type proportions of synthetic dataset consisting of 5:1 hindbrain-to-forebrain cells projected either by BrainSTEM or by DM. Proportion plots of in vitro–derived single-cell datasets across different time points and conditions showing ( F ) proportion of cells confidently assigned, ( G ) region.lineage proportions for confidently assigned cells, ( H ) cell-type proportions for confidently assigned cells, and ( I ) brain region proportions for confidently assigned DA neurons. ( J ) Ridge plots showing the distribution of dopaminergic neuron gene expression signature (DA N score) and line graphs showing the proportion of DA N in the midbrain-associated cells across different time points for selected in vitro midbrain differentiation time series studies. Spearman’s correlation coefficient for the DA N score and the proportion of DA N in each study presented. Two-sided Wilcoxon rank sum test applied to assess the pairwise difference between the in-house dataset and the other three datasets, with significance indicated by asterisk [ P value for the in-house dataset versus Fiorenzano et al. : 0.000, the in-house dataset versus Xu et al. : 0.078, and the in-house dataset versus You et al. : 0.779]. ( K ) Ridge plots showing the distribution of serotonergic neuron gene expression signature (Ser N score) in the hindbrain-associated cells in the same setting.

Figure Legend Snippet: ( A ) Schematic depicting the BrainSTEM framework’s two-tier mapping process of query datasets onto our fetal whole-brain atlas and midbrain subatlas. Created in BioRender. Toh, H. (2025); https://BioRender.com/pl47oha . Proportion plots of in vivo brain tissue single-cell studies across different developmental stages showing ( B ) proportion of cells confidently assigned, ( C ) region.lineage proportions for confidently assigned cells, and ( D ) cell-type proportions for confidently assigned cells. ( E ) Cell-type proportions of synthetic dataset consisting of 5:1 hindbrain-to-forebrain cells projected either by BrainSTEM or by DM. Proportion plots of in vitro–derived single-cell datasets across different time points and conditions showing ( F ) proportion of cells confidently assigned, ( G ) region.lineage proportions for confidently assigned cells, ( H ) cell-type proportions for confidently assigned cells, and ( I ) brain region proportions for confidently assigned DA neurons. ( J ) Ridge plots showing the distribution of dopaminergic neuron gene expression signature (DA N score) and line graphs showing the proportion of DA N in the midbrain-associated cells across different time points for selected in vitro midbrain differentiation time series studies. Spearman’s correlation coefficient for the DA N score and the proportion of DA N in each study presented. Two-sided Wilcoxon rank sum test applied to assess the pairwise difference between the in-house dataset and the other three datasets, with significance indicated by asterisk [ P value for the in-house dataset versus Fiorenzano et al. : 0.000, the in-house dataset versus Xu et al. : 0.078, and the in-house dataset versus You et al. : 0.779]. ( K ) Ridge plots showing the distribution of serotonergic neuron gene expression signature (Ser N score) in the hindbrain-associated cells in the same setting.

Techniques Used: In Vivo, In Vitro, Derivative Assay, Gene Expression

Ligation:

Article Title: A platform-agnostic evaluation of non-formalin fixed single cell RNA technologies
Article Snippet: .. Rosenberg and Roco developed the plate-based Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq) approach for fixed cells or nuclei, commercialized as the Parse Biosciences ‘Evercode Whole Transcriptome kit’ in 2021. , Parse (acquired by QIAGEN in 2025) subsequently introduced random hexamers to the v3 Evercode assay in addition to the oligo(T) primed 3’ capture that enables elevated representation of the gene body and a cell capture efficiency around 28%., , Similar to Parse, with an expected cell capture rate around 28%, Scale Biosciences (acquired by 10x Genomics in 2025) released a plate-based combinatorial indexing ‘RNA Single Cell Sequencing Kit’ with 3’ poly-A-capture on fixed cells or nuclei in 2022. .. Also in 2022, Fluent Biosciences (acquired by Illumina in 2024) released the Protein Interaction Profile Sequencing (PIP-Seq) method, with a purported 80% cell capture using an instrument-free approach for 3’ poly-A-capture within templated emulsions.

Sequencing:

Article Title: Endothelial tenascin signaling preserves VSMCs contractile phenotype in the human arterial wall in type II diabetes mellitus
Article Snippet: The cell suspensions were filtered through MACS ® SmartStrainers (30 μm) (Miltenyi Biotec, Germany) and collected by centrifugation at 500 × g for 5 min at 4 °C. .. For single-cell sequencing, dissociated cells were processed using the cell fixation (SB1001) and single-cell whole-transcriptome (SB2001) kits from Parse Biosciences, USA, according to the manufacturer’s instructions. .. Two libraries, each containing 5000 cells, were generated and sequenced via the Illumina NovaSeq PE150 platform (Illumina, USA) at 50,000 reads per cell.

Single Cell:

Article Title: Lateral hypothalamic input engages a disinhibitory microcircuit in the dorsal raphe to promote behavior activation
Article Snippet: .. Barcoded single-cell libraries were prepared from fixed single-cell suspensions using Evercode Whole Transcriptome v.2 (Parse Biosciences) following the manufacturer’s instructions. ..

Construct:

Article Title: Wasf1 deletion attenuates tau hyperphosphorylation, microglial state transition, and cognitive deficits in P301S tau mice
Article Snippet: .. snRNA-seq libraries were constructed using the Whole Transcriptome v3 kit (Parse Biosciences) following the manufacturer’s protocol. ..

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