genome analyzer sequence data preprocessing Search Results


analyzing 10x genomics rna sequencing data  (10X Genomics)
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10X Genomics analyzing 10x genomics rna sequencing data
(A) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO cortices at E12.5-P7. RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN, subplate excitatory neuron; IN, interneuron; OPC, oligodendrocyte precursor cell; EndoC, endothelial cell; MGC, microglial cell; MC, meningeal cell; postnatal NSC, postnatal neural stem cell; AS, astrocyte. (B) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices at different developmental stages (E12.5-E17.5). RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN; subplate excitatory neuron; IN, interneuron; MGC, microglial cell; EndoC, endothelial cell; MC, meningeal cell; OPC, oligodendrocyte precursor cell. (C) Developmental progression score analysis of the temporal identity of WT and Nfia;Nfix cDKO RGPs. (D) Quantification of the ratio of RGPs in G 1 phase of WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices across different embryonic stages. (E) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E12.5-E13.5 transition. (F) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E14.5-E15.5 transition. (G) Progressive dynamics of Nfia / NFIA (top) and Nfix / NFIX (bottom) expression in RGPs along aligned cortical development based on mouse (purple) or human (green) single-cell <t>RNA-seq</t> data (GSE104276) ( 99 ). Embryonic day (E); Gestational week (GW). (H) Luciferase assay using the Nfia (mouse) or NFIA (human) CRE-Luc reporter co-transfected with the indicated amounts of the same or different species-mouse or human NFIA expression plasmids (pCIG-NFIA) or control plasmids (pCAG-IRES-EGFP). Fold change of relative Luc activity was calculated by normalizing to the mean Luc activity level of empty Luc reporter co-transfected with pCIG plasmid control group. (n = 3 biological replicates for each group). Luc, luciferase. Data are presented as mean ± SD ( C) and mean ± SEM ( D-F and H) . *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Statistical analysis was performed using unpaired Student’s t-test (C) , Chi-square test (D) , and pairwise Wilcoxon rank sum test (E and F) , and One-way ANOVA (H) .
Analyzing 10x Genomics Rna Sequencing Data, 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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analyzing 10x genomics rna sequencing data - by Bioz Stars, 2026-07
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genome analyzer sequence data raw hisegtm sequence data  (Adaptive Biotechnologies Corp)
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Adaptive Biotechnologies Corp genome analyzer sequence data raw hisegtm sequence data
(A) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO cortices at E12.5-P7. RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN, subplate excitatory neuron; IN, interneuron; OPC, oligodendrocyte precursor cell; EndoC, endothelial cell; MGC, microglial cell; MC, meningeal cell; postnatal NSC, postnatal neural stem cell; AS, astrocyte. (B) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices at different developmental stages (E12.5-E17.5). RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN; subplate excitatory neuron; IN, interneuron; MGC, microglial cell; EndoC, endothelial cell; MC, meningeal cell; OPC, oligodendrocyte precursor cell. (C) Developmental progression score analysis of the temporal identity of WT and Nfia;Nfix cDKO RGPs. (D) Quantification of the ratio of RGPs in G 1 phase of WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices across different embryonic stages. (E) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E12.5-E13.5 transition. (F) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E14.5-E15.5 transition. (G) Progressive dynamics of Nfia / NFIA (top) and Nfix / NFIX (bottom) expression in RGPs along aligned cortical development based on mouse (purple) or human (green) single-cell <t>RNA-seq</t> data (GSE104276) ( 99 ). Embryonic day (E); Gestational week (GW). (H) Luciferase assay using the Nfia (mouse) or NFIA (human) CRE-Luc reporter co-transfected with the indicated amounts of the same or different species-mouse or human NFIA expression plasmids (pCIG-NFIA) or control plasmids (pCAG-IRES-EGFP). Fold change of relative Luc activity was calculated by normalizing to the mean Luc activity level of empty Luc reporter co-transfected with pCIG plasmid control group. (n = 3 biological replicates for each group). Luc, luciferase. Data are presented as mean ± SD ( C) and mean ± SEM ( D-F and H) . *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Statistical analysis was performed using unpaired Student’s t-test (C) , Chi-square test (D) , and pairwise Wilcoxon rank sum test (E and F) , and One-way ANOVA (H) .
Genome Analyzer Sequence Data Raw Hisegtm Sequence Data, supplied by Adaptive Biotechnologies Corp, 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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Image Search Results


(A) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO cortices at E12.5-P7. RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN, subplate excitatory neuron; IN, interneuron; OPC, oligodendrocyte precursor cell; EndoC, endothelial cell; MGC, microglial cell; MC, meningeal cell; postnatal NSC, postnatal neural stem cell; AS, astrocyte. (B) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices at different developmental stages (E12.5-E17.5). RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN; subplate excitatory neuron; IN, interneuron; MGC, microglial cell; EndoC, endothelial cell; MC, meningeal cell; OPC, oligodendrocyte precursor cell. (C) Developmental progression score analysis of the temporal identity of WT and Nfia;Nfix cDKO RGPs. (D) Quantification of the ratio of RGPs in G 1 phase of WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices across different embryonic stages. (E) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E12.5-E13.5 transition. (F) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E14.5-E15.5 transition. (G) Progressive dynamics of Nfia / NFIA (top) and Nfix / NFIX (bottom) expression in RGPs along aligned cortical development based on mouse (purple) or human (green) single-cell RNA-seq data (GSE104276) ( 99 ). Embryonic day (E); Gestational week (GW). (H) Luciferase assay using the Nfia (mouse) or NFIA (human) CRE-Luc reporter co-transfected with the indicated amounts of the same or different species-mouse or human NFIA expression plasmids (pCIG-NFIA) or control plasmids (pCAG-IRES-EGFP). Fold change of relative Luc activity was calculated by normalizing to the mean Luc activity level of empty Luc reporter co-transfected with pCIG plasmid control group. (n = 3 biological replicates for each group). Luc, luciferase. Data are presented as mean ± SD ( C) and mean ± SEM ( D-F and H) . *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Statistical analysis was performed using unpaired Student’s t-test (C) , Chi-square test (D) , and pairwise Wilcoxon rank sum test (E and F) , and One-way ANOVA (H) .

Journal: bioRxiv

Article Title: Dose-dependent NFI regulation of progenitor lifespan and output underlying human neocortical malformation

doi: 10.64898/2025.12.27.696675

Figure Lengend Snippet: (A) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO cortices at E12.5-P7. RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN, subplate excitatory neuron; IN, interneuron; OPC, oligodendrocyte precursor cell; EndoC, endothelial cell; MGC, microglial cell; MC, meningeal cell; postnatal NSC, postnatal neural stem cell; AS, astrocyte. (B) UMAP-dimension reduction of the expression profiles of individual cells obtained in WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices at different developmental stages (E12.5-E17.5). RGP, radial glial progenitor; IP, intermediate progenitor; imm EN, immature excitatory neuron; deep EN, deep layer excitatory neuron; upper EN, upper layer excitatory neuron; subplate EN; subplate excitatory neuron; IN, interneuron; MGC, microglial cell; EndoC, endothelial cell; MC, meningeal cell; OPC, oligodendrocyte precursor cell. (C) Developmental progression score analysis of the temporal identity of WT and Nfia;Nfix cDKO RGPs. (D) Quantification of the ratio of RGPs in G 1 phase of WT and Nfia;Nfix cDKO ( Nfi cDKO) cortices across different embryonic stages. (E) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E12.5-E13.5 transition. (F) Quantification showing a reduction in the magnitude of expression changes of downstream TFs and their target genes in Nfia;Nfix cDKO RGPs compared with WT control RGPs during E14.5-E15.5 transition. (G) Progressive dynamics of Nfia / NFIA (top) and Nfix / NFIX (bottom) expression in RGPs along aligned cortical development based on mouse (purple) or human (green) single-cell RNA-seq data (GSE104276) ( 99 ). Embryonic day (E); Gestational week (GW). (H) Luciferase assay using the Nfia (mouse) or NFIA (human) CRE-Luc reporter co-transfected with the indicated amounts of the same or different species-mouse or human NFIA expression plasmids (pCIG-NFIA) or control plasmids (pCAG-IRES-EGFP). Fold change of relative Luc activity was calculated by normalizing to the mean Luc activity level of empty Luc reporter co-transfected with pCIG plasmid control group. (n = 3 biological replicates for each group). Luc, luciferase. Data are presented as mean ± SD ( C) and mean ± SEM ( D-F and H) . *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Statistical analysis was performed using unpaired Student’s t-test (C) , Chi-square test (D) , and pairwise Wilcoxon rank sum test (E and F) , and One-way ANOVA (H) .

Article Snippet: For analyzing 10X Genomics RNA sequencing data of WT and Nfia;Nfix cDKO cortices, quality filtering of cell barcodes was first performed on the total counts of RNA reads and the percentage of mitochondrial genes.

Techniques: Expressing, Control, RNA Sequencing, Luciferase, Transfection, Activity Assay, Plasmid Preparation