Journal: Scientific Reports

Article Title: A human tau seeded neuronal cell model recapitulates molecular responses associated with Alzheimer’s disease

doi: 10.1038/s41598-022-06411-4

Figure Lengend Snippet: Probes used to validate RNA sequencing.

Article Snippet: Idi1 , Rn00585526_m1 , 4331182, FAM.

Techniques: Sequencing

Journal: Frontiers in Nutrition

Article Title: Prevention of high-fat/high-sugar diet-induced type 2 diabetes mellitus-associated non-alcoholic fatty liver disease in rats with fermented and raw Rosa roxburghii Tratt (Cili) juice

doi: 10.3389/fnut.2025.1584551

Figure Lengend Snippet: Expression analyses of transcription or protein levels of selected genes. (A) Expression analyses of selected genes by qRT–PCR. The data represent the means ± SDs from six biological replicates with three technical replicates. (B–D) FCJ/RCJ upregulated ABCC3, IDI1, and APOA2 expression in the liver. FCJ and RCJ significantly upregulated hepatic ABCC3 (B) and IDI1 (C) expression, and RCJ significantly upregulated hepatic APOA2 (D) expression in T2DM rats. The data represent the means ± SDs from three biological replicates with three technical replicates. * p < 0.05, *** p < 0.001, **** p < 0.0001.

Article Snippet: The western blotting antibodies used included APOA2 (BM5624, BOSTER, China), IDI1 (A07892-1, BOSTER, China), ABCC3 (DF3874, Affinity, United States), β-tubulin (Solarbio, China), goat anti-rabbit (BS13278, Bioworld, United States), and goat anti-mouse (BS12478, Bioworld, United States) antibodies.

Techniques: Expressing, Quantitative RT-PCR

Journal: eLife

Article Title: Histone deacetylase 3 represses cholesterol efflux during CD4 + T-cell activation

doi: 10.7554/eLife.70978

Figure Lengend Snippet:

Article Snippet: Sequence-based reagent , Idi1 , Thermo Fisher Scientific , #Mm01337454_m1 , .

Techniques: Flow Cytometry, Cell Culture, Blocking Assay, In Vitro, Recombinant, Staining, Isolation, Selection, Sequencing, Software

Journal: PLoS Biology

Article Title: Host Defense against Viral Infection Involves Interferon Mediated Down-Regulation of Sterol Biosynthesis

doi: 10.1371/journal.pbio.1000598

Figure Lengend Snippet: (A) The Sterol biosynthesis pathway shown in KEGG notation with abbreviated metabolites (abbreviations listed in ). The geranylgeranylation pathway responsible for GGPP synthesis is shown in the dashed box. (B) Heat map of the cholesterol biosynthesis temporal genes' expression during the first 12 h of mCMV infection (left panel) or IFNγ treatment (right panel). Each time point corresponds to one independent biological sample, and columns indicate time in hours. Fold changes of expression levels are represented on a Log2 scale compared to mock-treated cells, ranging from a 0.8× lower expression (dark blue) to a 1.2× higher expression (bright yellow). (C–H) Expression analysis measured by qRT-PCR of Hmgcs1 , Hmgcr , Idi1 , and Sqle genes in BMDM infected with mCMV(24 hpi) (C) or treated for 24 h with IFNγ (10 and 100 U/ml) (D), IFNβ (10 and 25 U/ml) (E), IL6 (10 and 25 U/ml) (F), IL1β (10 and 100 U/ml) (G), or TNF (10 and 100 U/ml) (H). Graphs show levels of mRNA expression of the respective genes either infected or cytokines-treated relative to mock samples. Bars represent the means ± SD of five independent experiments with biological triplicates for each experiment. * p <0.05, ** p <0.01, *** p <0.001, determined with an unpaired Student's t test.

Article Snippet: Taqman Primer probe sets were purchased from Applied Biosystems, Warrington, UK (Assay ID: Hmgcs1: Mm00524111-m1; Hmgcr: Mm01282499-m1; Idi1: Mm00836417-g1; Sqle: Mm00436772-A1).

Techniques: Expressing, Infection, Quantitative RT-PCR

Journal: PLoS Biology

Article Title: Host Defense against Viral Infection Involves Interferon Mediated Down-Regulation of Sterol Biosynthesis

doi: 10.1371/journal.pbio.1000598

Figure Lengend Snippet: (A) Heat map of expression levels of a set of genes after 24 h mock treatment, infection with Herpes simplex virus 1 (HSV1), Semliki forest virus (SFV), Vaccinia virus (VV), or Adenovirus (Ad) in BMDM . Genes represent the innate immunity activation, the MHC class II antigen presentation, and the cholesterol and unsaturated fatty acids biosynthesis. Each square represents a single biological replicate. Fold changes of expression levels are represented on a Log2 scale compared to mock-treated cells, ranging from a 0.4× lower expression (dark blue) to a 1.6× higher expression (bright yellow). (B) Expression analysis measured by qRT-PCR of Hmgcs1 , Hmgcr , Idi1 , and Sqle genes in BMDM after 24 h mock treatment, mCMV, or mCMVdie3 infection, respectively. Graphs show the level of expression of the indicated genes relative to mock-treated samples and bars represent mean ± SD of two independent experiments with triplicate biological measurements for each experiment. (C) BMDM were infected with mCMV or mock treated, and supernatant was collected after 8 h and directly added to fresh BMDM. After 24 h, RNA from these cultures was collected and Hmgcs1 , Hmgcr , and Sqle expression were measured by qRT-PCR. To test for the presence of any detectable virus, an aliquot of the supernatant was used to perform a standard plaque assay (no infectious virus detected, unpublished data). Graphs show the level of expression of the indicated genes relative to mock-treated samples and bars represent means ± SD of three independent experiments with triplicate biological measurements for each experiment. * p <0.05, ** p <0.01, *** p <0.001, determined with an unpaired Student's t test.

Article Snippet: Taqman Primer probe sets were purchased from Applied Biosystems, Warrington, UK (Assay ID: Hmgcs1: Mm00524111-m1; Hmgcr: Mm01282499-m1; Idi1: Mm00836417-g1; Sqle: Mm00436772-A1).

Techniques: Expressing, Infection, Virus, Activation Assay, Immunopeptidomics, Quantitative RT-PCR, Plaque Assay

Journal: PLoS Biology

Article Title: Host Defense against Viral Infection Involves Interferon Mediated Down-Regulation of Sterol Biosynthesis

doi: 10.1371/journal.pbio.1000598

Figure Lengend Snippet: (A–C) Wild type BMDM or BMDM from IFNβ−/− knockout mice or from IFNAR1−/− knockout mice were mock treated, infected with mCMV, or treated with IFNβ (10 U/ml) for 24 h. RNA was collected and the gene expression of Hmgcs1 , Hmgcr , Idi1 , and Sqle was measured by qRT-PCR. Graphs show the level of expression of the indicated genes relative to mock-treated samples. Bars represent the mean ± SD of biological quadruplicates. (D) Wild type BMDM or BMDM from IFNAR1−/− knockout mice were infected with mCMV or treated with IFNβ (10 U/ml). After 48 h, free cholesterol concentration was measured by enzymatic assay . Bars represent the mean ± SD of biological quadruplicates. * p <0.05, ** p <0.01, *** p <0.001, determined with an unpaired Student's t test.

Article Snippet: Taqman Primer probe sets were purchased from Applied Biosystems, Warrington, UK (Assay ID: Hmgcs1: Mm00524111-m1; Hmgcr: Mm01282499-m1; Idi1: Mm00836417-g1; Sqle: Mm00436772-A1).

Techniques: Knock-Out, Infection, Gene Expression, Quantitative RT-PCR, Expressing, Concentration Assay, Enzymatic Assay