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cellranger version 7 1 0 10x genomics  (10X Genomics)
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10X Genomics cellranger version 7 1 0 10x genomics
Figure 1. Improved perturbation assignment to single nuclei with T7-assisted sgRNA library prep and an engineered CROP-seq vector (A) Schematic of Multiome Perturb-seq experimental design, library, and guide assignment strategy. sgRNA identity transcripts are biased toward nuclear retention by addition of dual SIRLOIN elements flanking the sgRNA cassette (purple), and a partial <t>10x</t> TSO capture sequence (green) assists recovery. Tran- scripts are linearly amplified via an internal high-activity T7 promoter from barcoded cDNA. U6, modified U6 Pol III promoter, LB: lineage barcode cassette. (B) Percentage of single nuclei assigned to 1, 2, or 3+ sgRNA identities using traditional CROP-seq or T7-assisted library prep, in a standard CROP-seq vector with T7 promoter (SIRLOIN/TSO) or a CROP-seq vector with T7 promoter, dual SIRLOINs and partial TSO capture sequence (+SIRLOIN/TSO), at indicated sequencing depths (downsampled for comparison, deeper sequencing for downstream analysis). (C) Density of UMI and total sequencing reads of sgRNA identity transcripts amplified by traditional CROP-seq or T7-assisted library prep in nuclei-containing droplets, in each vector condition, downsampled to equal sequencing depth per nucleus. (D) Average single-cell expression and promoter accessibility of perturbation target genes in NTC-assigned populations vs. populations assigned to each perturbation. Error bars show 95% confidence intervals. (E) Average normalized expression of perturbation target genes in perturbed subpopulations. (F) Pseudobulk normalized accessibility at promoters of perturbation target genes in perturbed subpopulations.
Cellranger Version 7 1 0 10x Genomics, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Figure 1. Improved perturbation assignment to single nuclei with T7-assisted sgRNA library prep and an engineered CROP-seq vector (A) Schematic of Multiome Perturb-seq experimental design, library, and guide assignment strategy. sgRNA identity transcripts are biased toward nuclear retention by addition of dual SIRLOIN elements flanking the sgRNA cassette (purple), and a partial 10x TSO capture sequence (green) assists recovery. Tran- scripts are linearly amplified via an internal high-activity T7 promoter from barcoded cDNA. U6, modified U6 Pol III promoter, LB: lineage barcode cassette. (B) Percentage of single nuclei assigned to 1, 2, or 3+ sgRNA identities using traditional CROP-seq or T7-assisted library prep, in a standard CROP-seq vector with T7 promoter (SIRLOIN/TSO) or a CROP-seq vector with T7 promoter, dual SIRLOINs and partial TSO capture sequence (+SIRLOIN/TSO), at indicated sequencing depths (downsampled for comparison, deeper sequencing for downstream analysis). (C) Density of UMI and total sequencing reads of sgRNA identity transcripts amplified by traditional CROP-seq or T7-assisted library prep in nuclei-containing droplets, in each vector condition, downsampled to equal sequencing depth per nucleus. (D) Average single-cell expression and promoter accessibility of perturbation target genes in NTC-assigned populations vs. populations assigned to each perturbation. Error bars show 95% confidence intervals. (E) Average normalized expression of perturbation target genes in perturbed subpopulations. (F) Pseudobulk normalized accessibility at promoters of perturbation target genes in perturbed subpopulations.

Journal: Cell systems

Article Title: Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome.

doi: 10.1016/j.cels.2024.12.002

Figure Lengend Snippet: Figure 1. Improved perturbation assignment to single nuclei with T7-assisted sgRNA library prep and an engineered CROP-seq vector (A) Schematic of Multiome Perturb-seq experimental design, library, and guide assignment strategy. sgRNA identity transcripts are biased toward nuclear retention by addition of dual SIRLOIN elements flanking the sgRNA cassette (purple), and a partial 10x TSO capture sequence (green) assists recovery. Tran- scripts are linearly amplified via an internal high-activity T7 promoter from barcoded cDNA. U6, modified U6 Pol III promoter, LB: lineage barcode cassette. (B) Percentage of single nuclei assigned to 1, 2, or 3+ sgRNA identities using traditional CROP-seq or T7-assisted library prep, in a standard CROP-seq vector with T7 promoter (SIRLOIN/TSO) or a CROP-seq vector with T7 promoter, dual SIRLOINs and partial TSO capture sequence (+SIRLOIN/TSO), at indicated sequencing depths (downsampled for comparison, deeper sequencing for downstream analysis). (C) Density of UMI and total sequencing reads of sgRNA identity transcripts amplified by traditional CROP-seq or T7-assisted library prep in nuclei-containing droplets, in each vector condition, downsampled to equal sequencing depth per nucleus. (D) Average single-cell expression and promoter accessibility of perturbation target genes in NTC-assigned populations vs. populations assigned to each perturbation. Error bars show 95% confidence intervals. (E) Average normalized expression of perturbation target genes in perturbed subpopulations. (F) Pseudobulk normalized accessibility at promoters of perturbation target genes in perturbed subpopulations.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Cellranger-arc version 2.0.2 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Cellranger version 7.1.0 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest perturbseq Norman et al.56 https://github.com/thomasmaxwellnorman/ perturbseq_demo/tree/master/perturbseq Scanpy version 1.9.3 Wolf et al.57 https://doi.org/10.1186/s13059-017-1382-0, https://scanpy.readthedocs.io/en/stable/ index.html SnapATAC2 version 2.6.0 Zhang et al.58 https://doi.org/10.1038/s41592-023-02139-9, https://kzhang.org/SnapATAC2/ AutoGluon version 1.1.1 Erickson et al.47 https://doi.org/10.48550/arXiv.2003.06505, https://auto.gluon.ai/stable/index.html Other DMEM-F12 Gibco Cat#11320033 Fetal bovine serum VWR Cat#97068-085 Penicillin-Streptomycin Gibco Cat#15140122 Hygromycin B ThermoFisher Scientific Cat#10687-010 Bovine serum albumin Sigma Cat#A9418

Techniques: Plasmid Preparation, Sequencing, Activity Assay, Comparison, Expressing