software for generating an automatic measurement sequence and for processing the measurement results obtained Search Results


human smscs  (Selleck Chemicals)
94
Selleck Chemicals human smscs
Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in <t>human</t> <t>SMSCs</t> after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.
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transcript assemblertm software  (Paracel BLAST)
90
Paracel BLAST transcript assemblertm software
Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in <t>human</t> <t>SMSCs</t> after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.
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clc_bio bioinformatic software  (CLC Bio)
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Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in <t>human</t> <t>SMSCs</t> after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.
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gcg sequence analysis software package  (Pharmacopeia Inc)
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Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in <t>human</t> <t>SMSCs</t> after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.
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basecalling software guppy 5.0.1  (Oxford Nanopore)
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Oxford Nanopore basecalling software guppy 5.0.1
Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in <t>human</t> <t>SMSCs</t> after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.
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commercial sequencing services  (Lark Technologies Inc)
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Lark Technologies Inc commercial sequencing services
Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in <t>human</t> <t>SMSCs</t> after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.
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mrna magnetic isolation module  (New England Biolabs)
99
New England Biolabs mrna magnetic isolation module
Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in <t>human</t> <t>SMSCs</t> after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.
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rapid barcoding kit  (Oxford Nanopore)
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Oxford Nanopore rapid barcoding kit
Schematic representation of mechanistic strategies of <t>barcoding.</t> (A–C) Barcodes can be introduced to a template using adaptors through direct ligation (A) , using RT- or PCR primers at the reverse transcription or PCR amplification step (B) , and using hybridizing molecular inversion probes (C) . (D) Schematic representation of the difference between “barcodes” and “sample indexes”. Barcodes aim to correct sequencing errors. For example, a misreading nucleotide, guanosine (G) can be corrected in final consensus sequences for a pool of Sample 1 (top panel). Sample indexes are used to multiplex different sequencing amplicons generated from different pools of samples (Sample 1, 2, and 3) (bottom panel). Panel (A) is modified based on in and panel (C) is modified based on in .
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nebnext ultratm ii dna library prep kit for illumina new england biolabs  (New England Biolabs)
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Schematic representation of mechanistic strategies of <t>barcoding.</t> (A–C) Barcodes can be introduced to a template using adaptors through direct ligation (A) , using RT- or PCR primers at the reverse transcription or PCR amplification step (B) , and using hybridizing molecular inversion probes (C) . (D) Schematic representation of the difference between “barcodes” and “sample indexes”. Barcodes aim to correct sequencing errors. For example, a misreading nucleotide, guanosine (G) can be corrected in final consensus sequences for a pool of Sample 1 (top panel). Sample indexes are used to multiplex different sequencing amplicons generated from different pools of samples (Sample 1, 2, and 3) (bottom panel). Panel (A) is modified based on in and panel (C) is modified based on in .
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Image Search Results


Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in human SMSCs after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Journal: Science advances

Article Title: Meniscal fibrocartilage regeneration inspired by meniscal maturational and regenerative process.

doi: 10.1126/sciadv.adg8138

Figure Lengend Snippet: Fig. 4. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) RNA-seq analyses in human SMSCs after static and CTS treatment [(A1) volcano plot of differentially expressed genes (DEGs) in CTS group versus static group; (A2) KEGG pathway enrichment, red boxes represent Hippo and TGFβ signaling]. (B) Volcano plot of differentially expressed genes in regenerated tissue of PCL scaffold + synovium transplant group versus native porcine menisci [(B1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (B2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (B3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (C) Heatmap of differential gene cluster in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (C2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (C3) PCL scaffold + synovium transplant group at 2 versus 4 months]. (D) KEGG pathway enrichment in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(D1) PCL scaffold + synovium transplant group 2M versus native menisci of sham group; (D2) PCL scaffold + synovium transplant group 4M versus native menisci of sham group; (D3) PCL scaffold + synovium transplant group at 2 versus 4 months, the red boxes represent Hippo and TGFβ signaling]. (E) Protein and mRNA levels in human SMSCs after static and CTS treatment [(E1) Western blot analysis; (E2) semiquantitative analysis of Western blot, n = 3, unpaired t test; (E3) mRNA levels, n = 8, unpaired t test]. (F) Cell immunofluorescence of human SMSCs after static and CTS treatment [(F1) cell immunofluorescence; (F2) six regions are randomly selected for semiquantitative analysis; the intensity of immunofluorescence is calculated by ImageJ software, n = 6, unpaired t test] (continued with Fig. 5). **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Article Snippet: To inhibit phosphorylation of Smad3, human SMSCs were treated with 5 μM SIS3 HCL (S7959, Selleck) for 4 hours.

Techniques: RNA Sequencing, Western Blot, Immunofluorescence, Software

Fig. 5. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) Protein and mRNA levels in human SMSCs after being treated with dihy- drexidine and SIS3 [(A1) the Western blot analysis; (A2) the semiquantitative analysis of Western blot, n = 3, one-way ANOVA; (A3) the alcian blue staining; (A4) the semiquantitative analysis of alcian blue staining, n = 3, one-way ANOVA; (A5) cell immunofluorescence; (A6) the semiquantitative analysis of cell immunofluorescence, Dihy represents dihydrexidine, n = 6, one-way ANOVA; (A7) the mRNA levels, n = 8, one-way ANOVA]. (B) Immunofluorescent colocalization of YAP and Smad2/3 in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(B1) immunofluorescent colocalization of YAP and Smad2/3; (B2) immu- nofluorescence overlap coefficient, n = 9]. (C) Immunofluorescent colocalization of pSmad2/3 and SOX9 in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) immunofluorescent colocalization of pSmad2/3 and SOX9; (C2) immunofluorescence overlap coefficient, n = 9]. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Journal: Science advances

Article Title: Meniscal fibrocartilage regeneration inspired by meniscal maturational and regenerative process.

doi: 10.1126/sciadv.adg8138

Figure Lengend Snippet: Fig. 5. The identification of YAP-pSmad2/3-SOX9 axis during MSCs chondrogenesis. (A) Protein and mRNA levels in human SMSCs after being treated with dihy- drexidine and SIS3 [(A1) the Western blot analysis; (A2) the semiquantitative analysis of Western blot, n = 3, one-way ANOVA; (A3) the alcian blue staining; (A4) the semiquantitative analysis of alcian blue staining, n = 3, one-way ANOVA; (A5) cell immunofluorescence; (A6) the semiquantitative analysis of cell immunofluorescence, Dihy represents dihydrexidine, n = 6, one-way ANOVA; (A7) the mRNA levels, n = 8, one-way ANOVA]. (B) Immunofluorescent colocalization of YAP and Smad2/3 in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(B1) immunofluorescent colocalization of YAP and Smad2/3; (B2) immu- nofluorescence overlap coefficient, n = 9]. (C) Immunofluorescent colocalization of pSmad2/3 and SOX9 in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) immunofluorescent colocalization of pSmad2/3 and SOX9; (C2) immunofluorescence overlap coefficient, n = 9]. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Article Snippet: To inhibit phosphorylation of Smad3, human SMSCs were treated with 5 μM SIS3 HCL (S7959, Selleck) for 4 hours.

Techniques: Western Blot, Staining, Immunofluorescence

Fig. 6. Piezo1 mediates mechanotransduction on YAP-pSmad2/3-SOX9 axis through concerted activation of calcineurin and NFATc1 during MSCs chondro- genesis. (A) Protein and mRNA levels of Piezo1 in human SMSCs after static and CTS treatment [(A1) the Western blot analysis; (A2) the semiquantitative analysis of Western blot, n = 3, unpaired t test; (A3) the cell immunofluorescence; (A4) the semiquantitative analysis of cell immunofluorescence, n = 6, unpaired t test; (A5) the mRNA levels, n = 8, unpaired t test]. (B) Immunofluorescent assessment of Piezo1 expression in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci. (C) Protein and mRNA levels in human SMSCs after being treated with YODA1 or GsMTx-4 [(C1) the Western blot analysis; (C2) the semiquantitative analysis of Western blot, n = 3, one-way ANOVA; (C3) the mRNA levels, n = 8, unpaired t test; (C4) the alcian blue staining; (C5) the semiquantitative analysis of alcian blue staining, n = 3, one-way ANOVA; (C6) the cell immunofluorescence; (C7) the semiquantitative analysis of cell immunofluorescence, n = 6, one-way ANOVA]. (D) Assessment of intracellular calcium content in human SMSCs [(D1) intracellular calcium content after static and CTS treatment; (D2) the semiquantitative analysis of calcium content, n = 5, unpaired t test; (D3) intracellular calcium content after being treated with YODA1 or GsMTx-4; (D4) the semiquantitative analysis of calcium content, n = 5, one-way ANOVA]. (E) Protein and mRNA levels in human SMSCs after CsA treatment [(E1) Western blot analysis, the red arrow represents dephosphorylated NFATc1, the blue arrows represent phosphorylated NFATc1; (E2) the semiquantitative analysis of Western blot, n = 3, one-way ANOVA; (E3) the alcian blue staining; (E4) the semiquantitative analysis of alcian blue staining, n = 3, one-way ANOVA; (E5) the mRNA levels, n = 8, unpaired t test; (E6) the cell immunofluorescence; (E7) the semiquantitative analysis of cell immunofluorescence, n = 6, one-way ANOVA]. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Journal: Science advances

Article Title: Meniscal fibrocartilage regeneration inspired by meniscal maturational and regenerative process.

doi: 10.1126/sciadv.adg8138

Figure Lengend Snippet: Fig. 6. Piezo1 mediates mechanotransduction on YAP-pSmad2/3-SOX9 axis through concerted activation of calcineurin and NFATc1 during MSCs chondro- genesis. (A) Protein and mRNA levels of Piezo1 in human SMSCs after static and CTS treatment [(A1) the Western blot analysis; (A2) the semiquantitative analysis of Western blot, n = 3, unpaired t test; (A3) the cell immunofluorescence; (A4) the semiquantitative analysis of cell immunofluorescence, n = 6, unpaired t test; (A5) the mRNA levels, n = 8, unpaired t test]. (B) Immunofluorescent assessment of Piezo1 expression in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci. (C) Protein and mRNA levels in human SMSCs after being treated with YODA1 or GsMTx-4 [(C1) the Western blot analysis; (C2) the semiquantitative analysis of Western blot, n = 3, one-way ANOVA; (C3) the mRNA levels, n = 8, unpaired t test; (C4) the alcian blue staining; (C5) the semiquantitative analysis of alcian blue staining, n = 3, one-way ANOVA; (C6) the cell immunofluorescence; (C7) the semiquantitative analysis of cell immunofluorescence, n = 6, one-way ANOVA]. (D) Assessment of intracellular calcium content in human SMSCs [(D1) intracellular calcium content after static and CTS treatment; (D2) the semiquantitative analysis of calcium content, n = 5, unpaired t test; (D3) intracellular calcium content after being treated with YODA1 or GsMTx-4; (D4) the semiquantitative analysis of calcium content, n = 5, one-way ANOVA]. (E) Protein and mRNA levels in human SMSCs after CsA treatment [(E1) Western blot analysis, the red arrow represents dephosphorylated NFATc1, the blue arrows represent phosphorylated NFATc1; (E2) the semiquantitative analysis of Western blot, n = 3, one-way ANOVA; (E3) the alcian blue staining; (E4) the semiquantitative analysis of alcian blue staining, n = 3, one-way ANOVA; (E5) the mRNA levels, n = 8, unpaired t test; (E6) the cell immunofluorescence; (E7) the semiquantitative analysis of cell immunofluorescence, n = 6, one-way ANOVA]. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Article Snippet: To inhibit phosphorylation of Smad3, human SMSCs were treated with 5 μM SIS3 HCL (S7959, Selleck) for 4 hours.

Techniques: Activation Assay, Western Blot, Immunofluorescence, Expressing, Staining

Fig. 7. The effect of matrix stiffness on YAP-pSmad2/3-SOX9 axis. (A) Protein and mRNA levels in human SMSCs after being treated with soft or stiff matrix [(A1) the mechanical properties of silicon rubber and polystyrene culture plate, n = 3; (A2) Western blot analysis, the red arrow indicates dephosphorylated NFATc1, the blue arrows indicate phosphorylated NFATc1; (A3) the semiquantitative analysis of Western blot, n = 3, unpaired t test; (A4) the alcian blue staining; (A5) the semiquantitative analysis of alcian blue staining, n = 3, unpaired t test; (A6) the mRNA levels, n = 8, unpaired t test]. (B) Immunofluorescent assessment of FAK in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(B1) the immunofluorescence of FAK; (B2) the semiquantitative analysis of FAK, n = 6, one-way ANOVA]. (C) Immunofluorescent assessment of pFAK in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) the immunofluorescence of pFAK; (C2) the semiquantitative analysis of pFAK, n = 6, one-way ANOVA]. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Journal: Science advances

Article Title: Meniscal fibrocartilage regeneration inspired by meniscal maturational and regenerative process.

doi: 10.1126/sciadv.adg8138

Figure Lengend Snippet: Fig. 7. The effect of matrix stiffness on YAP-pSmad2/3-SOX9 axis. (A) Protein and mRNA levels in human SMSCs after being treated with soft or stiff matrix [(A1) the mechanical properties of silicon rubber and polystyrene culture plate, n = 3; (A2) Western blot analysis, the red arrow indicates dephosphorylated NFATc1, the blue arrows indicate phosphorylated NFATc1; (A3) the semiquantitative analysis of Western blot, n = 3, unpaired t test; (A4) the alcian blue staining; (A5) the semiquantitative analysis of alcian blue staining, n = 3, unpaired t test; (A6) the mRNA levels, n = 8, unpaired t test]. (B) Immunofluorescent assessment of FAK in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(B1) the immunofluorescence of FAK; (B2) the semiquantitative analysis of FAK, n = 6, one-way ANOVA]. (C) Immunofluorescent assessment of pFAK in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci [(C1) the immunofluorescence of pFAK; (C2) the semiquantitative analysis of pFAK, n = 6, one-way ANOVA]. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Article Snippet: To inhibit phosphorylation of Smad3, human SMSCs were treated with 5 μM SIS3 HCL (S7959, Selleck) for 4 hours.

Techniques: Western Blot, Staining, Immunofluorescence

Fig. 8. The biomechanical stimulus and matrix stiffness regulate the expression of collagen cross-link enzymes (LOX and LH) through Piezo1. (A) Protein and mRNA levels of LOX and LH in human SMSCs after static or CTS treatment [(A1) the Western blot analysis; (A2) the semiquantitative analysis of LOX, n = 3, unpaired t test; (A3) the semiquantitative analysis of LH2, n = 3, unpaired t test; (A4) the cell immunofluorescence of LOX; (A5) the semiquantitative analysis of LOX immunofluorescence, n = 6, unpaired t test; (A6) the cell immunofluorescence of LH2; (A7) the semiquantitative analysis of LH2 immunofluorescence, n = 6, unpaired t test; (A8) the mRNA levels, n = 8, unpaired t test]. (B) Protein and mRNA levels of LOX and LH in human SMSCs after being treated with YODA1 or GsMTx-4 [(B1) the Western blot analysis; (B2) the semiquantitative analysis of LOX, n = 3, one-way ANOVA; (B3) the semiquantitative analysis of LH2, n = 3, one-way ANOVA; (B4) the cell immunofluorescence of LOX; (B5) the semiquantitative analysis of LOX immunofluorescence, n = 6, one-way ANOVA; (B6) the cell immunofluorescence of LH2; (B7) the semiquantitative analysis of LH2 immunofluorescence, n = 6, one-way ANOVA; (B8) the mRNA levels, n = 8, one-way ANOVA]. (C) Protein and mRNA levels of LOX and LH in human SMSCs after being treated with soft or stiff matrix [(C1) the Western blot analysis; (C2) the semiquantitative analysis of LOX, n = 3, unpaired t test; (C3) the semiquantitative analysis of LH2, n = 3, unpaired t test; (C4) the mRNA levels, n = 8, unpaired t test]. (D) Immunofluorescent assessment of LOX expression in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci. (E) Immunofluorescent assessment of LH2 expression in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Journal: Science advances

Article Title: Meniscal fibrocartilage regeneration inspired by meniscal maturational and regenerative process.

doi: 10.1126/sciadv.adg8138

Figure Lengend Snippet: Fig. 8. The biomechanical stimulus and matrix stiffness regulate the expression of collagen cross-link enzymes (LOX and LH) through Piezo1. (A) Protein and mRNA levels of LOX and LH in human SMSCs after static or CTS treatment [(A1) the Western blot analysis; (A2) the semiquantitative analysis of LOX, n = 3, unpaired t test; (A3) the semiquantitative analysis of LH2, n = 3, unpaired t test; (A4) the cell immunofluorescence of LOX; (A5) the semiquantitative analysis of LOX immunofluorescence, n = 6, unpaired t test; (A6) the cell immunofluorescence of LH2; (A7) the semiquantitative analysis of LH2 immunofluorescence, n = 6, unpaired t test; (A8) the mRNA levels, n = 8, unpaired t test]. (B) Protein and mRNA levels of LOX and LH in human SMSCs after being treated with YODA1 or GsMTx-4 [(B1) the Western blot analysis; (B2) the semiquantitative analysis of LOX, n = 3, one-way ANOVA; (B3) the semiquantitative analysis of LH2, n = 3, one-way ANOVA; (B4) the cell immunofluorescence of LOX; (B5) the semiquantitative analysis of LOX immunofluorescence, n = 6, one-way ANOVA; (B6) the cell immunofluorescence of LH2; (B7) the semiquantitative analysis of LH2 immunofluorescence, n = 6, one-way ANOVA; (B8) the mRNA levels, n = 8, one-way ANOVA]. (C) Protein and mRNA levels of LOX and LH in human SMSCs after being treated with soft or stiff matrix [(C1) the Western blot analysis; (C2) the semiquantitative analysis of LOX, n = 3, unpaired t test; (C3) the semiquantitative analysis of LH2, n = 3, unpaired t test; (C4) the mRNA levels, n = 8, unpaired t test]. (D) Immunofluorescent assessment of LOX expression in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci. (E) Immunofluorescent assessment of LH2 expression in regenerated tissue of PCL scaffold + synovium transplant group and native porcine menisci. *P < 0.05, **P < 0.01, ***P < 0.0005, ****P < 0.0001; ns, not significant.

Article Snippet: To inhibit phosphorylation of Smad3, human SMSCs were treated with 5 μM SIS3 HCL (S7959, Selleck) for 4 hours.

Techniques: Expressing, Western Blot, Immunofluorescence

Schematic representation of mechanistic strategies of barcoding. (A–C) Barcodes can be introduced to a template using adaptors through direct ligation (A) , using RT- or PCR primers at the reverse transcription or PCR amplification step (B) , and using hybridizing molecular inversion probes (C) . (D) Schematic representation of the difference between “barcodes” and “sample indexes”. Barcodes aim to correct sequencing errors. For example, a misreading nucleotide, guanosine (G) can be corrected in final consensus sequences for a pool of Sample 1 (top panel). Sample indexes are used to multiplex different sequencing amplicons generated from different pools of samples (Sample 1, 2, and 3) (bottom panel). Panel (A) is modified based on in and panel (C) is modified based on in .

Journal: Frontiers in Molecular Biosciences

Article Title: A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level

doi: 10.3389/fmolb.2023.1141534

Figure Lengend Snippet: Schematic representation of mechanistic strategies of barcoding. (A–C) Barcodes can be introduced to a template using adaptors through direct ligation (A) , using RT- or PCR primers at the reverse transcription or PCR amplification step (B) , and using hybridizing molecular inversion probes (C) . (D) Schematic representation of the difference between “barcodes” and “sample indexes”. Barcodes aim to correct sequencing errors. For example, a misreading nucleotide, guanosine (G) can be corrected in final consensus sequences for a pool of Sample 1 (top panel). Sample indexes are used to multiplex different sequencing amplicons generated from different pools of samples (Sample 1, 2, and 3) (bottom panel). Panel (A) is modified based on in and panel (C) is modified based on in .

Article Snippet: Primer-associated approach , Sequence-based barcodes , SQK-RBK004: transposase carrying barcodes to the site of the cleavage , - , - , Whole genome , Oxford Nanopore Rapid Barcoding kit (SQK-RBK004) , SARS-CoV-2 patient samples (nasopharyngeal swab) , Oxford Nanopore , Guppy version 3.6.0; ARTIC Network bioinformatics protocol , Multiplex samples , Propose a method to sequence the whole genome of SARS-CoV-2 in a rapid and cost-efficient manner , .

Techniques: Ligation, Reverse Transcription, Amplification, Sequencing, Multiplex Assay, Generated, Modification

Systematic comparison of barcoding strategies used in the category of molecular barcodes.

Journal: Frontiers in Molecular Biosciences

Article Title: A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level

doi: 10.3389/fmolb.2023.1141534

Figure Lengend Snippet: Systematic comparison of barcoding strategies used in the category of molecular barcodes.

Article Snippet: Primer-associated approach , Sequence-based barcodes , SQK-RBK004: transposase carrying barcodes to the site of the cleavage , - , - , Whole genome , Oxford Nanopore Rapid Barcoding kit (SQK-RBK004) , SARS-CoV-2 patient samples (nasopharyngeal swab) , Oxford Nanopore , Guppy version 3.6.0; ARTIC Network bioinformatics protocol , Multiplex samples , Propose a method to sequence the whole genome of SARS-CoV-2 in a rapid and cost-efficient manner , .

Techniques: Comparison, Software, Sequencing, Multiplex Assay, CRISPR, Plasmid Preparation, Microarray, Binding Assay, Amplification, Extraction, Ligation, DNA Sequencing, Multiplexing, Generated, Reverse Transcription, Staining, Flow Cytometry, High Throughput Screening Assay, Inhibition, Blocking Assay, Conjugation Assay, RNA Sequencing Assay, Transmission Assay, Incubation, Diagnostic Assay, Next-Generation Sequencing, Infection

Journal: Cell

Article Title: A trans -complementation system for SARS-CoV-2 recapitulates authentic viral replication without virulence

doi: 10.1016/j.cell.2021.02.044

Figure Lengend Snippet:

Article Snippet: BsaI restriction endonuclease , New England Biolabs , Cat#R3733S.

Techniques: Recombinant, SYBR Green Assay, Electroporation, Gel Extraction, Electron Microscopy, Synthesized, Sequencing, Software

KEY RESOURCES TABLE

Journal: Cell systems

Article Title: Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics

doi: 10.1016/j.cels.2017.05.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Total RNA was extracted either by Trizol (Life Technologies) per manufacturer protocol or using QIAgen RNeasy kit (QIAgen, Germantown, MD, USA). mRNA was further purified from isolated total RNA by poly(A) separation using Oligo (dT) 25 Magnetic Beads kit (New England BioLabs, Ipswich, MA, USA) per manufacturer protocol.

Techniques: Recombinant, Sequencing, Modification, Magnetic Beads, Bicinchoninic Acid Protein Assay, Cell Viability Assay, Caspase-Glo Assay, Clone Assay, Amplification, Software