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genomics suite rna-seq analysis pipeline  (Partek)

 
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    Partek genomics suite rna-seq analysis pipeline
    ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) <t>RNA-Seq</t> of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.
    Genomics Suite Rna Seq Analysis Pipeline, supplied by Partek, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/rna-seq+analysis+pipeline/pmc11290974-214-22-21?v=Partek
    Average 90 stars, based on 1 article reviews
    genomics suite rna-seq analysis pipeline - by Bioz Stars, 2026-06
    90/100 stars

    Images

    1) Product Images from "The IFITM5 mutation in osteogenesis imperfecta type V is associated with an ERK/SOX9-dependent osteoprogenitor differentiation defect"

    Article Title: The IFITM5 mutation in osteogenesis imperfecta type V is associated with an ERK/SOX9-dependent osteoprogenitor differentiation defect

    Journal: The Journal of Clinical Investigation

    doi: 10.1172/JCI170369

    ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.
    Figure Legend Snippet: ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.

    Techniques Used: Mutagenesis, Injection, RNA Sequencing Assay, Expressing, Control



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    ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) <t>RNA-Seq</t> of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.
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    ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) <t>RNA-Seq</t> of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.
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    Image Search Results


    ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.

    Journal: The Journal of Clinical Investigation

    Article Title: The IFITM5 mutation in osteogenesis imperfecta type V is associated with an ERK/SOX9-dependent osteoprogenitor differentiation defect

    doi: 10.1172/JCI170369

    Figure Lengend Snippet: ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.

    Article Snippet: Differential gene expression analysis was performed using DESeq2, and statistical significance was determined by 2-way ANOVA, which is built into the Partek Genomics Suite RNA-Seq analysis pipeline.

    Techniques: Mutagenesis, Injection, RNA Sequencing Assay, Expressing, Control

    ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.

    Journal: The Journal of Clinical Investigation

    Article Title: The IFITM5 mutation in osteogenesis imperfecta type V is associated with an ERK/SOX9-dependent osteoprogenitor differentiation defect

    doi: 10.1172/JCI170369

    Figure Lengend Snippet: ( A – B ) Lineage tracing of chondrocytes coexpressing mutant Ifitm5 and Ai9 reporter in Rosa 26 mIfitm5/Ai9 Acan-Cre ERT2 mice. Tamoxifen injection was performed at P10, and bones were collected after 3 weeks (at 5 weeks of age). Representative images of the proximal tibia ( A ) and the tibia diaphyseal area ( B ) Decreased fraction of Ai9 + cells migrated to the bone diaphysis in mutant animals compared with littermate controls ( n = 3 per genotype; n = 2–3 fields counted per sample; * P = 0.03, by 2-tailed Student’s t test). Original magnification, ×20. ( C ) RNA-Seq of total femoral cDNA from Rosa26 mIfitm5/+ Acan-Cre ERT2 mice ( n = 3 per genotype) showed enrichment for chondrogenic gene expression in the mutant samples by GO term analysis. ( D ) Heatmap of focused differential gene expression analysis from RNA-Seq, showing upregulation of chondrogenic gene markers and decreased expression of osteogenic markers in the mutants compared with the control group.

    Article Snippet: Normalization, differential expression, hierarchical clustering, and GO analysis were then performed using the RNA-Seq analysis pipeline in Partek Genomics Suite (Partek).

    Techniques: Mutagenesis, Injection, RNA Sequencing Assay, Expressing, Control