5 parametric logistic curve equations graphpad prism 10.2.2 Search Results


statistical software version 19.5.1  (MedCalc Software Ltd)
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Statistical Software Version 19.5.1, supplied by MedCalc Software Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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paper dhcr24 ko hepg2 sc5d ko synthego  (Synthego Inc)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
Paper Dhcr24 Ko Hepg2 Sc5d Ko Synthego, supplied by Synthego Inc, 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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resource source identifier oligonucleotides htrpc6 f  (Azenta)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
Resource Source Identifier Oligonucleotides Htrpc6 F, supplied by Azenta, 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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plx3397 diet  (Plexxikon)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
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sigmastat 3 5  (SYSTAT)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
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sigmaplot 14 5  (SYSTAT)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
Sigmaplot 14 5, supplied by SYSTAT, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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statistical software version 16 1  (STATA Corporation)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
Statistical Software Version 16 1, supplied by STATA Corporation, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
Minianalysis, supplied by synaptosoft inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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image lab software  (Bio-Rad)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
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glomax multiple detection system  (Promega)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
Glomax Multiple Detection System, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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resource source identifier cdc42 forward 5  (Addgene inc)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
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addgene plasmid  (Addgene inc)
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Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control <t>HepG2</t> cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, <t>DHCR24</t> KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and <t>SC5D).</t> Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S
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Image Search Results


Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control HepG2 cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, DHCR24 KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and SC5D). Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S

Journal: iScience

Article Title: Knockouts of CYP51A1 , DHCR24 , or SC5D from cholesterol synthesis reveal pathways modulated by sterol intermediates.

doi: 10.1016/j.isci.2024.110651

Figure Lengend Snippet: Figure 1. Expression of CRISPR-Cas9 targeted mRNA and proteins in control HepG2 cells (Native) and in knockout cells of enzymes from the late part of cholesterol synthesis (CYP51 KO, DHCR24 KO, SCD KO) See Figure S2 for Sanger sequence of selected clones and Table S1 targeted gene region and predicted effect of indel on protein. Bars represent the mean G SD of three replicates from different cell culture wells. (A) Relative mRNA expression of targeted genes (CYP51, DHCR24, and SC5D). Expression data were normalized to ACTB, GAPDH, and RPLP0 reference genes (See Table S2 for primers used). (B) Targeted protein expression by WB (CYP51A1, DHCR24, SC5D, Total SREBP2, H—nuclear - n-SREBP2). 10 mg of proteins were loaded and normalized to total proteins (for un-cropped full blots see Figure S8; Table S3 for antibodies used). (C) A simplified cholesterol synthesis, with measured sterols from the post-lanosterol part of a synthesis and the position of deleted enzymes in red. The Bloch and Kandutsch-Russell sterol pathways are indicated (See Figure S1 for detailed synthesis pathway; Figure S3 for sterol synthesis in individual genotypes). (D–G) represent sterols analysis by LC-MS. Sterol concentrations are represented as a mean G SD (n = 4) and normalized to total amount of proteins (For result normalized to cell number are represented in Table S4). (D) Sterols and epoxylanosterol isolated from control and KO HepG2 cells with concentration normalize to total proteins. (E) Sterols isolated from culture medium. Result medium represent sterols from culture medium used in experiments (DMED +10% LDS +1% P/S

Article Snippet: HepG2 DHCR24 KO Synthego/This paper DHCR24 KO HepG2 SC5D KO Synthego/This paper SC5D KO Software and algorithms GraphPad Prism 10.2.2 https://www.graphpad.com GraphPad Software Venny 2.0 https://bioinfogp.cnb.csic.es/tools/venny/index.htm Venny 2.0 Biorender https://www.biorender.com/ Biorender ToppGene Suite https://toppgene.cchmc.org/ ToppGene Suite

Techniques: Expressing, CRISPR, Control, Knock-Out, Sequencing, Clone Assay, Cell Culture, Liquid Chromatography with Mass Spectroscopy, Isolation, Concentration Assay

Figure 2. Differential gene expression (DEG) using Clarium S microarrays (A) PCA (Principal component analysis) of raw gene expression data for all four conditions (Native, CYP51 KO, DHCR24 KO, and SC5D KO), each measurement in three replicates from different cell culture wells. (B) Number of up, down, and total differently expressed genes in all three genotypes compare to the Native HepG2 cell line after false discovery rate (FDR) correction (adj pvalue<0.05). (C) Venn diagram of DEGs comparing gene expression between different genotypes. (D) Venn diagram of changed KEGG pathways comparing different genotypes.

Journal: iScience

Article Title: Knockouts of CYP51A1 , DHCR24 , or SC5D from cholesterol synthesis reveal pathways modulated by sterol intermediates.

doi: 10.1016/j.isci.2024.110651

Figure Lengend Snippet: Figure 2. Differential gene expression (DEG) using Clarium S microarrays (A) PCA (Principal component analysis) of raw gene expression data for all four conditions (Native, CYP51 KO, DHCR24 KO, and SC5D KO), each measurement in three replicates from different cell culture wells. (B) Number of up, down, and total differently expressed genes in all three genotypes compare to the Native HepG2 cell line after false discovery rate (FDR) correction (adj pvalue<0.05). (C) Venn diagram of DEGs comparing gene expression between different genotypes. (D) Venn diagram of changed KEGG pathways comparing different genotypes.

Article Snippet: HepG2 DHCR24 KO Synthego/This paper DHCR24 KO HepG2 SC5D KO Synthego/This paper SC5D KO Software and algorithms GraphPad Prism 10.2.2 https://www.graphpad.com GraphPad Software Venny 2.0 https://bioinfogp.cnb.csic.es/tools/venny/index.htm Venny 2.0 Biorender https://www.biorender.com/ Biorender ToppGene Suite https://toppgene.cchmc.org/ ToppGene Suite

Techniques: Gene Expression, Cell Culture

Figure 3. Transcription factor enrichment analysis using ChEA 2022 and TransFac 2.0 (A) The top 20 enriched TFs from each KO cell line were used for visualization of ChEA data. (B) The Venn diagram of enriched TFs from ChEA analysis, (C) The Venn diagram of enriched TFs from TransFac 2.0 analysis. Number of TFs are in each group is represented. % indicates the fraction of all TFs in this analysis (m.i.—muscle initiator), (D) Common differentially expressed gene in HepG2 and mouse liver specific CYP51A1 KO. Red dots represent upregulated, blue dots downregulated genes and gray dots genes up and downregulated in both experiments. See Figure S12 for enriched KEGG pathways in mouse Cyp51 KO.

Journal: iScience

Article Title: Knockouts of CYP51A1 , DHCR24 , or SC5D from cholesterol synthesis reveal pathways modulated by sterol intermediates.

doi: 10.1016/j.isci.2024.110651

Figure Lengend Snippet: Figure 3. Transcription factor enrichment analysis using ChEA 2022 and TransFac 2.0 (A) The top 20 enriched TFs from each KO cell line were used for visualization of ChEA data. (B) The Venn diagram of enriched TFs from ChEA analysis, (C) The Venn diagram of enriched TFs from TransFac 2.0 analysis. Number of TFs are in each group is represented. % indicates the fraction of all TFs in this analysis (m.i.—muscle initiator), (D) Common differentially expressed gene in HepG2 and mouse liver specific CYP51A1 KO. Red dots represent upregulated, blue dots downregulated genes and gray dots genes up and downregulated in both experiments. See Figure S12 for enriched KEGG pathways in mouse Cyp51 KO.

Article Snippet: HepG2 DHCR24 KO Synthego/This paper DHCR24 KO HepG2 SC5D KO Synthego/This paper SC5D KO Software and algorithms GraphPad Prism 10.2.2 https://www.graphpad.com GraphPad Software Venny 2.0 https://bioinfogp.cnb.csic.es/tools/venny/index.htm Venny 2.0 Biorender https://www.biorender.com/ Biorender ToppGene Suite https://toppgene.cchmc.org/ ToppGene Suite

Techniques:

Figure 4. Proliferation and cell cycle analysis of HepG2 cell lines Plots represent the proliferation of HepG2 cell lines in different serum and cholesterol conditions on (A) FBS, (B) LDS +30 mg/mL cholesterol and (C) LDS. See Table S5 for sterol composition of FBS and LDS. The assay was performed using the CCK8 method and data are represented as mean G SEM (n = 6). Statistical significance was tested using One-way ANOVA with comparison to control, the native cell line result at the same time point, p value - *< 0.05, **< 0.01, ***< 0.001, ****<0.0001. Cell cycle measurements using propidium iodide are represented on (D) as a direct measurement and on (E) results normalized to total cell number (100%) and statistically evaluated. All KOs were compared with control native cell line using the statistical test described above. See Figure S7 for individual genotype proliferation and additional cholesterol concentration tested.

Journal: iScience

Article Title: Knockouts of CYP51A1 , DHCR24 , or SC5D from cholesterol synthesis reveal pathways modulated by sterol intermediates.

doi: 10.1016/j.isci.2024.110651

Figure Lengend Snippet: Figure 4. Proliferation and cell cycle analysis of HepG2 cell lines Plots represent the proliferation of HepG2 cell lines in different serum and cholesterol conditions on (A) FBS, (B) LDS +30 mg/mL cholesterol and (C) LDS. See Table S5 for sterol composition of FBS and LDS. The assay was performed using the CCK8 method and data are represented as mean G SEM (n = 6). Statistical significance was tested using One-way ANOVA with comparison to control, the native cell line result at the same time point, p value - *< 0.05, **< 0.01, ***< 0.001, ****<0.0001. Cell cycle measurements using propidium iodide are represented on (D) as a direct measurement and on (E) results normalized to total cell number (100%) and statistically evaluated. All KOs were compared with control native cell line using the statistical test described above. See Figure S7 for individual genotype proliferation and additional cholesterol concentration tested.

Article Snippet: HepG2 DHCR24 KO Synthego/This paper DHCR24 KO HepG2 SC5D KO Synthego/This paper SC5D KO Software and algorithms GraphPad Prism 10.2.2 https://www.graphpad.com GraphPad Software Venny 2.0 https://bioinfogp.cnb.csic.es/tools/venny/index.htm Venny 2.0 Biorender https://www.biorender.com/ Biorender ToppGene Suite https://toppgene.cchmc.org/ ToppGene Suite

Techniques: Cell Cycle Assay, Comparison, Control, Concentration Assay