Journal: The Journal of Neuroscience

Article Title: Neural Stem/Progenitor Cells Participate in the Regenerative Response to Perinatal Hypoxia/Ischemia

doi: 10.1523/JNEUROSCI.1898-05.2006

Figure Lengend Snippet: Primer sets used in RT-PCR

Article Snippet: Only those genes that were induced or repressed at least twofold in each replication are listed in supplemental (available at www.jneurosci.org as supplemental material ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Transcript Primers EGFR (TaqMan) Applied Biosystems TaqMan Assay ID Rn00580398_m1 Notch1 (Lux) 5′-CAC GTA CTG CGA GCT GCC CTA CG[FAM]G-3′ 5′-GGC AGG TGC CTC CGT TCT-3′ 18S (TaqMan) Applied Biosystems TaqMan Assay ID Hs99999901_s1 18S (Lux) Invitrogen catalog #115HM-01 Open in a separate window Primer sets used in RT-PCR

Techniques: TaqMan Assay

Journal: The Journal of Neuroscience

Article Title: Neural Stem/Progenitor Cells Participate in the Regenerative Response to Perinatal Hypoxia/Ischemia

doi: 10.1523/JNEUROSCI.1898-05.2006

Figure Lengend Snippet: Signaling pathways involved in control of NSP fate are induced by perinatal H/I. Ipsilateral H/I and control hemispheres were dissected out after 48 h of recovery. A, Total RNA was isolated and amplified by qRT-PCR using primers specific for EGFR and Notch1 and normalized to expression of 18S. Values in parentheses indicate CV for the target gene in the sample groups; n = 10 for ipsilateral and contralateral conditions, and n = 4 for sham condition. *p < 0.05 versus sham; †p < 0.05 versus contralateral by pairwise fixed reallocation randomization. Immunostaining for Notch1 was performed on cryostat sections from H/I (B) and control (C) animals. In situ hybridization was performed on cryostat sections of contralateral (D, G), ipsilateral (E, H), and control (F, I) hemispheres using a digoxigenin-labeled RNA probe for Hes5 (D–F) and Hes1 (G–I). Arrows in E delineate the region of increased Hes5 expression. Inset in E shows high-magnification 100× Nomarski image of the Hes5+ region showing a subependymal Hes5+ cell body (arrowhead) with processes (arrow) projecting through the ependyma. There was no evident change in Hes1 expression. Scale bars: inset in E, 4 μm; F, 10 μm. cp, Choroid plexus; V, ventricle.

Article Snippet: Only those genes that were induced or repressed at least twofold in each replication are listed in supplemental (available at www.jneurosci.org as supplemental material ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Transcript Primers EGFR (TaqMan) Applied Biosystems TaqMan Assay ID Rn00580398_m1 Notch1 (Lux) 5′-CAC GTA CTG CGA GCT GCC CTA CG[FAM]G-3′ 5′-GGC AGG TGC CTC CGT TCT-3′ 18S (TaqMan) Applied Biosystems TaqMan Assay ID Hs99999901_s1 18S (Lux) Invitrogen catalog #115HM-01 Open in a separate window Primer sets used in RT-PCR

Techniques: Protein-Protein interactions, Control, Isolation, Amplification, Quantitative RT-PCR, Expressing, Immunostaining, In Situ Hybridization, Labeling

Journal: Inflammatory Intestinal Diseases

Article Title: Hypoxia Reduces the Transcription of Fibrotic Markers in the Intestinal Mucosa

doi: 10.1159/000513061

Figure Lengend Snippet: TaqMan gene expression assays

Article Snippet: Relative mRNA expression was determined by the comparative ∆∆Ct method using beta-actin (ACTB) as the reference gene. table ft1 table-wrap mode="anchored" t5 Table 2 caption a7 Gene Full name TaqMan assay ID Human genes TGFβ Transforming growth factor beta Hs00998133_m1 ACTA2 Actin alpha 2, smooth muscle Hs00426835_g1 VIM Vimentin Hs00185584_m1 CDH1 Cadherin 1 Hs01023895_m1 CDH2 Cadherin 2 Hs00983056_m1 COL1A1 Collagen type I alpha 1 chain Hs00164004_m1 COL3A1 Collagen type III alpha 1 chain Hs00943809_m1 COL4A1 Collagen type IV alpha 1 chain Hs00266237_m1 MMP2 Matrix metallopeptidase 2 Hs01548727_m1 MMP3 Matrix metallopeptidase 3 Hs00968305_m1 MMP9 Matrix metallopeptidase 9 Hs00957562_m1 TIMP1 Tissue inhibitor of metalloproteinase 1 Hs01092512_g1 Mouse genes TGFβ Transforming growth factor beta Mm00524541_m1 ACTA2 Actin alpha 2, smooth muscle Mm00725412_s1 VIM Vimentin Mm01333430_m1 CDH1 Cadherin 1 Mm01247357_m1 CDH2 Cadherin 2 Mm01162497_m1 COL1A1 Collagen type I alpha 1 chain Mm00801666_g1 COL3A1 Collagen type III alpha 1 chain Mm00802300_m1 COL4A1 Collagen type IV alpha 1 chain Mm01210125_m1 MMP2 Matrix metallopeptidase 2 Mm00439498_m1 MMP3 Matrix metallopeptidase 3 Mm00440295_m1 MMP9 Matrix metallopeptidase 9 Mm00442991_m1 MMP13 Matrix metallopeptidase 13 Mm00439491_m1 TIMP1 Tissue inhibitor of metalloproteinase 1 Mm01341361_m1 Open in a separate window TaqMan gene expression assays Western Blot Total protein was harvested in M-PER lysis buffer (Thermo Fisher Scientific) supplemented with protease inhibitors (Roche Diagnostics, Mannheim, Germany).

Techniques: Gene Expression, TaqMan Assay

Journal: Journal of materials science. Materials in medicine

Article Title: Microsphere-Based Scaffolds Encapsulating Tricalcium Phosphate And Hydroxyapatite For Bone Regeneration

doi: 10.1007/s10856-016-5734-1

Figure Lengend Snippet: Genes used for RT-qPCR analysis

Article Snippet: For quantification, the BLANK constructs at week 0 were designated as the calibrator group and GAPDH expression as the endogenous control. table ft1 table-wrap mode="anchored" t5 caption a7 Gene Symbol TaqMan Assay ID Glyceraldehyde 3-phosphate dehydrogenase GAPDH Rn01775763_g1 Collagen type I COL1A1 Rn01463848_m1 Runt-related transcription factor 2 RUNX2 Rn01512298_m1 Bone gamma- carboxyglutamate protein BGLAP Rn00566386_g1 Integrin-binding sialoprotein IBSP Rn00561414_m1 Open in a separate window Genes used for RT-qPCR analysis 2.10 Histology and Immunohistochemistry (IHC) At 6 weeks, microsphere-based constructs (n = 3) were soaked in 30% w/v sucrose (Thermofisher Scientific, Waltham, MA) solution in PBS for 24 h. Afterward, the constructs were equilibrated in optimal cutting temperature embedding medium (OCT, Tissue-Tek, Torrance, CA) overnight at 37°C and then frozen at −20°C.

Techniques: TaqMan Assay

Journal: Tissue Engineering. Part A

Article Title: In Vitro Osteogenic Potential of Human Mesenchymal Stem Cells Is Predicted by Runx2/Sox9 Ratio

doi: 10.1089/ten.tea.2014.0096

Figure Lengend Snippet: Primers/Probes Used for Real-Time Polymerase Chain Reaction

Article Snippet: Data analysis was performed using ddCT values, which were determined by normalization to 18S rRNA and samples harvested on day 0. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene Forward primer Reverse primer Probe Applied biosystem reference number Runx2 AAG CAG TAT TTA CAA CAG AGG GTA CAA G GGT GCT CGG ATC CCA AAA CAT CAA ACA GCC TCT TCA GCA CAG TGA CAC Sox9 Hs00165814_m1 18S 431089E Open in a separate window Primers/Probes Used for Real-Time Polymerase Chain Reaction RNA interference The Neon Transfection System (Invitrogen) was used to transfect hMSCs (990V, 40 ms, 1 pulse) with 600 nM Sox9 (buffer concentration, OriGene).

Techniques:

Journal: Tissue Engineering. Part A

Article Title: In Vitro Osteogenic Potential of Human Mesenchymal Stem Cells Is Predicted by Runx2/Sox9 Ratio

doi: 10.1089/ten.tea.2014.0096

Figure Lengend Snippet: Sox9 gene expression of (A) on day 2 and 7 (n=12); (B) on day 14 and 21 (n=4), based on expression fold change to day 0 (mean±SEM *p<0.05); (C) Sox9 protein analysis: western blot and image analysis on day 7 either in control or dexamethasone (DEX) medium. Laminin B 1 served as internal control; one representative donor (n=3).

Article Snippet: Data analysis was performed using ddCT values, which were determined by normalization to 18S rRNA and samples harvested on day 0. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene Forward primer Reverse primer Probe Applied biosystem reference number Runx2 AAG CAG TAT TTA CAA CAG AGG GTA CAA G GGT GCT CGG ATC CCA AAA CAT CAA ACA GCC TCT TCA GCA CAG TGA CAC Sox9 Hs00165814_m1 18S 431089E Open in a separate window Primers/Probes Used for Real-Time Polymerase Chain Reaction RNA interference The Neon Transfection System (Invitrogen) was used to transfect hMSCs (990V, 40 ms, 1 pulse) with 600 nM Sox9 (buffer concentration, OriGene).

Techniques: Gene Expression, Expressing, Western Blot, Control

Journal: Tissue Engineering. Part A

Article Title: In Vitro Osteogenic Potential of Human Mesenchymal Stem Cells Is Predicted by Runx2/Sox9 Ratio

doi: 10.1089/ten.tea.2014.0096

Figure Lengend Snippet: Runx2 gene expression (A) on day 2 and 7 (n=12); (B) on day 14 and 21 (n=4); Runx2/Sox9 ratio (C) on day 2 and 7 (n=12), (D) on day 14 and 21 (n=4), based on expression fold change to day 0 (mean±SEM *p<0.05).

Article Snippet: Data analysis was performed using ddCT values, which were determined by normalization to 18S rRNA and samples harvested on day 0. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene Forward primer Reverse primer Probe Applied biosystem reference number Runx2 AAG CAG TAT TTA CAA CAG AGG GTA CAA G GGT GCT CGG ATC CCA AAA CAT CAA ACA GCC TCT TCA GCA CAG TGA CAC Sox9 Hs00165814_m1 18S 431089E Open in a separate window Primers/Probes Used for Real-Time Polymerase Chain Reaction RNA interference The Neon Transfection System (Invitrogen) was used to transfect hMSCs (990V, 40 ms, 1 pulse) with 600 nM Sox9 (buffer concentration, OriGene).

Techniques: Gene Expression, Expressing

Journal: Tissue Engineering. Part A

Article Title: In Vitro Osteogenic Potential of Human Mesenchymal Stem Cells Is Predicted by Runx2/Sox9 Ratio

doi: 10.1089/ten.tea.2014.0096

Figure Lengend Snippet: (A) Runx2/Sox9 ratio on day 7 (mean±SEM *p<0.05); (B) 45Ca incorporation on day 28 (mean±SEM *p<0.05), (C) alkaline phosphatase (ALP) activity on day 14, for 8 representative donors with low (n=4) and high (n=4) osteogenic potential (high osteogenic potential defined as above 100,000 CPMI/μg DNA on day 28; low osteogenic potential as below 80,000 CPMI/μg DNA on day 28); (D) ALP activity for donors with both low and high osteogenic potential (n=8); (E) correlation of 45Ca incorporation on day 28 with Runx2/Sox9 ratio on day 7; for unselected population of donors (n=12).

Article Snippet: Data analysis was performed using ddCT values, which were determined by normalization to 18S rRNA and samples harvested on day 0. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene Forward primer Reverse primer Probe Applied biosystem reference number Runx2 AAG CAG TAT TTA CAA CAG AGG GTA CAA G GGT GCT CGG ATC CCA AAA CAT CAA ACA GCC TCT TCA GCA CAG TGA CAC Sox9 Hs00165814_m1 18S 431089E Open in a separate window Primers/Probes Used for Real-Time Polymerase Chain Reaction RNA interference The Neon Transfection System (Invitrogen) was used to transfect hMSCs (990V, 40 ms, 1 pulse) with 600 nM Sox9 (buffer concentration, OriGene).

Techniques: Activity Assay

Journal: Tissue Engineering. Part A

Article Title: In Vitro Osteogenic Potential of Human Mesenchymal Stem Cells Is Predicted by Runx2/Sox9 Ratio

doi: 10.1089/ten.tea.2014.0096

Figure Lengend Snippet: (A) Electroporation of hMSCs with Sox9 siRNA, gene expression after 48 h based on expression fold change to day 0; *indicates significant difference between Sox9 siRNA and controls (n=6, mean±SEM, *p<0.05), (B) protein analysis: western blot and image analysis of Sox9 protein after Sox9 siRNA electroporation (48 h) in control medium. Laminin B 1 served as internal control; one representative donor (n=3); (C) Runx2/Sox9 ratio after 48 h, one representative donor; (D) 45Ca incorporation on day 28 either in control or DEX medium; *indicates significant difference between Sox9 siRNA treatment and scrambled control and control, respectively (n=6, mean±SEM, *p<0.05); (E) staining of alizarin red S on day 28 after Sox9 siRNA treatment, either in control or DEX medium; representative images (scale bar: 200 μm); (F) optical density graphs in DEX medium; *indicates significant difference between Sox9 siRNA and control groups (n=6, mean±SEM *p<0.05). Color images available online at www.liebertpub.com/tea

Article Snippet: Data analysis was performed using ddCT values, which were determined by normalization to 18S rRNA and samples harvested on day 0. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene Forward primer Reverse primer Probe Applied biosystem reference number Runx2 AAG CAG TAT TTA CAA CAG AGG GTA CAA G GGT GCT CGG ATC CCA AAA CAT CAA ACA GCC TCT TCA GCA CAG TGA CAC Sox9 Hs00165814_m1 18S 431089E Open in a separate window Primers/Probes Used for Real-Time Polymerase Chain Reaction RNA interference The Neon Transfection System (Invitrogen) was used to transfect hMSCs (990V, 40 ms, 1 pulse) with 600 nM Sox9 (buffer concentration, OriGene).

Techniques: Electroporation, Gene Expression, Expressing, Western Blot, Control, Staining

Journal: Journal of Assisted Reproduction and Genetics

Article Title: Maternal obesity in mice not only affects fresh embryo quality but also aggravates injury due to vitrification

doi: 10.1007/s10815-016-0790-5

Figure Lengend Snippet: Assay IDs and GenBank sequence accession numbers for expression assays used for real-time RT-PCR

Article Snippet: All primers were shown to have comparable amplification efficiencies against the internal control. table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Gene Assay ID b GenBank sequence accession number Atf4 Mm00515325_g1 {"type":"entrez-nucleotide","attrs":{"text":"NM_009716.2","term_id":"121949820","term_text":"NM_009716.2"}} NM_009716.2 Grp78 Mm00517690_g1 {"type":"entrez-nucleotide","attrs":{"text":"NM_001163434.1","term_id":"254540167","term_text":"NM_001163434.1"}} NM_001163434.1 Hsp70 Mm03038954_s1 {"type":"entrez-nucleotide","attrs":{"text":"NM_010478.2","term_id":"124339825","term_text":"NM_010478.2"}} NM_010478.2 MnSOD Mm01313000_m1 {"type":"entrez-nucleotide","attrs":{"text":"NM_013671.3","term_id":"76253932","term_text":"NM_013671.3"}} NM_013671.3 p53 Mm01731290_g1 {"type":"entrez-nucleotide","attrs":{"text":"NM_001127233.1","term_id":"187960039","term_text":"NM_001127233.1"}} NM_001127233.1 Gadd45g Mm01352550_g1 {"type":"entrez-nucleotide","attrs":{"text":"NM_011817.2","term_id":"254553385","term_text":"NM_011817.2"}} NM_011817.2 caspase-3 Mm01195085_m1 {"type":"entrez-nucleotide","attrs":{"text":"NM_009810.2","term_id":"118129865","term_text":"NM_009810.2"}} NM_009810.2 IGF-II Mm00439564_m1 {"type":"entrez-nucleotide","attrs":{"text":"NM_001122736.1","term_id":"170172555","term_text":"NM_001122736.1"}} NM_001122736.1 ZO-1 Mm00493699_m1 {"type":"entrez-nucleotide","attrs":{"text":"NM_001122736.1","term_id":"170172555","term_text":"NM_001122736.1"}} NM_001122736.1 E-cadherin Mm01247357_m1 {"type":"entrez-nucleotide","attrs":{"text":"NM_009864.2","term_id":"118129809","term_text":"NM_009864.2"}} NM_009864.2 GAPDH a Mm99999915_g1 {"type":"entrez-nucleotide","attrs":{"text":"NM_008084.2","term_id":"126012538","term_text":"NM_008084.2"}} NM_008084.2 Open in a separate window a GAPDH was used as an internal control b Primer sets were TaqMan® gene expression assays Assay IDs and GenBank sequence accession numbers for expression assays used for real-time RT-PCR Relative gene expression was calculated using the ∆∆CT [ 27 ] method.

Techniques: Sequencing, Expressing

Journal: Neuropharmacology

Article Title: Chronic stress induces cell type-selective transcriptomic and electrophysiological changes in the bed nucleus of the stria terminalis

doi: 10.1016/j.neuropharm.2019.03.013

Figure Lengend Snippet: Normalized quantities of mRNA for the Gria1 (Type I: NS n = 18, CSS n = 17; Type II: NS n = 32, CSS n = 22; Type III: NS n = 27, CSS n = 22; A) and Gria2 subunits (Type I: NS n = 18, CSS n = 17; Type II: NS n = 31, CSS n = 24; Type III: NS n = 25, CSS n = 22; B) from cells classified as Type I-III from NS (grey open squares; 20 rats) and CSS (black closed squares; 19 rats) rats. Used Mann-Whitney U-tests. Mean and SEM shown. * p < 0.002

Article Snippet: Results were analyzed using the ΔCt method ( Livak and Schmittgen 2001 , Vandesompele, De Preter et al. 2002 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene name (protein name) TaqMan assay reference Grial (GluRl) Rn00709588_m1 Gria2 (GluR2) Rn00568514_m1 Gria3 (GluR3) Rn00583547_m1 Gria4 (GluR4) Rn00568544_m1 Crh (CRF) Rn01462137_m1 Ptpn5 (STEP) Rn01480059_m1 Ppp1ca (PP1A) Rn00580546_m1 Ppp1cb (PP1B) Rn00565033_m1 Ppp1cc (PP1C) Rn04339209_m1 Ppp3ca (Calcineurin A) Rn00690508_m1 Ppp3cb (Calcineurin B) Rn00566864_m1 Ppp3cc (Calcineurin C) Rn01465907_m1 Ppp1r1b (DARPP-32) Rn01452984_m1 Open in a separate window List of gene names and TaqMan reference numbers.

Techniques: MANN-WHITNEY

Journal: Toxicology and applied pharmacology

Article Title: Embryoid body test with morphological and molecular endpoints implicates potential developmental toxicity of trans -resveratrol

doi: 10.1016/j.taap.2018.07.006

Figure Lengend Snippet: Chemicals used for the present study

Article Snippet: The preparation of cis -resveratrol may contain 1–5% of trans -resveratrol, according to the product information of the supplier ( www.caymanchem.com/product/10004235 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig. 1. caption a7 The chemical structures of the compounds evaluated in the present study (A), and the experimental scheme to assess the morphogenetic and molecular impact of compound exposures using P19C5 embryoid bodies (B). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Compound Name CASRN Vendor (catalog number) Stock concentration *1 Figures *2 trans -Resveratrol 501-36-0 Selleck (L2900; Anti-diabetes Compound Library) 10 mM Santa Cruz (200808) 50 mM , , Cayman (70675) 10 mM , cis -Resveratrol 61434-67-1 Cayman (10004235) 10 mM , Resveratrol-3-O-sulfate 858127-11-4 Cayman (14942) 10 mM , Resve ratrol-3-O-D-glucuronide 387372-17-0 Cayman (13832) 10 mM , Resveratrol-4’-O-D-glucuronide 387372-20-5 Cayman (13833) 10 mM , Diethylstilbestrol 56-53-1 Santa Cruz (204720) 50 mM Raloxifene 82640-04-8 Santa Cruz (204230) 50 mM SRT1720 925434-55-5 Sigma-Aldrich (567860) 10 mM EX527 49843-98-3 Sigma-Aldrich (E7034) 50 mM Aphidicolin 38966-21-1 Cayman (14007) 1 mM , Hydroxyurea 127-07-1 Sigma-Aldrich (H8627) 100 mM , Open in a separate window CASRN, Chemical Abstracts Service Registry Number *1 All compounds are dissolved in dimethyl sulfoxide (DMSO), except for hydroxyurea (dissolved in H2O) *2 Figure numbers that show experimental data using the corresponding chemical stocks Chemicals used for the present study 2.2.

Techniques: Concentration Assay, Drug discovery, Two-Dimensional Gel Electrophoresis

Journal: Physiological Genomics

Article Title: Microarray analysis of aging-associated immune system alterations in the rostral ventrolateral medulla of F344 rats

doi: 10.1152/physiolgenomics.00131.2016

Figure Lengend Snippet: List of immune system genes used for quantitative PCR validation of microarray analysis and their TaqMan assay IDs

Article Snippet: Actb, Hprt1, Ldha , and Rplp1 genes were used as endogenous controls and the geometric average of their Ct values was used to calculate each gene’s ΔCt value ( 1 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Functional Category Gene Symbol TaqMan Assay ID Complement system C1qa Rn01519903_m1 C1qc(C1qg) Rn01516757_m1 Cd93(C1qr1) Rn00584525_g1 C3 Rn00584525_g1 C4a Rn00566466_m1 Cfd Rn00709527_m1 Cfh Rn01535436_g1 Vwf Rn00590326_m1 Klkb1 Rn01488161_m1 Microglial cells Cd14 Rn00572656_g1 Cd68 Rn01495634_g1 Tlr2 Rn02133647_s1 Cx3cr1 Rn02134446_s1 Trem2 Rn01512170_m1 Fcrl2 Rn01455191_m1 B2m Rn00560865_m1 Endogenous controls Actb Rn00667869_m1 Hprt1 Rn01527840_m1 Ldha Rn00820751_g1 Rplp1 Rn03467157_gH Open in a separate window List of immune system genes used for quantitative PCR validation of microarray analysis and their TaqMan assay IDs Microarray Data Analysis Hybridization signal intensities from microarrays were extracted with Agilent Feature Extraction Software, version 9.5.1.1. (Agilent Technologies) (Gene Expression Omnibus accession number {"type":"entrez-geo","attrs":{"text":"GSE90956","term_id":"90956"}} GSE90956 ).

Techniques: Real-time Polymerase Chain Reaction, Biomarker Discovery, Microarray, TaqMan Assay