gene exp dyx1c1 ccpg1 hs00370049 m1  (Thermo Fisher)


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    Structured Review

    Thermo Fisher gene exp dyx1c1 ccpg1 hs00370049 m1
    Knockdown of RFX1 , RFX2 , and RFX3 affect the expression of <t>DYX1C1</t> and DCDC2 but not KIAA0319 in hTERT-RPE1 cells. A ) Binding of RFX1 and RFX2 to the X-box motifs present in DYX1C1 and DCDC2 promoters. Biotinylated probes spanning the X-box motifs were incubated with nuclear extracts from serum-starved hTERT-RPE1 cells with or without antibodies (ab) against RFX1, RFX2, and RFX3. Supershifts for both probes were detected for RFX1 and RFX2 antibodies (white arrowheads). One representative experiment of 3 is shown. B ) Fold-change differences in the expression of DCGs upon knockdown of RFX TFs. By using siRNA against RFX1 , RFX2 , and RFX3 , alone or in different combinations, genes were silenced in hTERT-RPE1 cells. Cells were thereafter starved for 24 h to induce ciliogenesis, and expression levels of DYX1C1 , DCDC2 , and KIAA0319 were measured by using qRT-PCR. C ) Fold-change difference in expression levels of RFX1 , RFX2 , and RFX3 upon siRNA silencing. qRT-PCR data are summarized by using the ΔΔC t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem . Significance of the post hoc tests after ANOVA is presented as *** P ≤ 0.001, ** P ≤ 0.01, * P ≤ 0.05 after multiple correction of simultaneous comparisons.
    Gene Exp Dyx1c1 Ccpg1 Hs00370049 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs"

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs

    Journal: The FASEB Journal

    doi: 10.1096/fj.201500124RR

    Knockdown of RFX1 , RFX2 , and RFX3 affect the expression of DYX1C1 and DCDC2 but not KIAA0319 in hTERT-RPE1 cells. A ) Binding of RFX1 and RFX2 to the X-box motifs present in DYX1C1 and DCDC2 promoters. Biotinylated probes spanning the X-box motifs were incubated with nuclear extracts from serum-starved hTERT-RPE1 cells with or without antibodies (ab) against RFX1, RFX2, and RFX3. Supershifts for both probes were detected for RFX1 and RFX2 antibodies (white arrowheads). One representative experiment of 3 is shown. B ) Fold-change differences in the expression of DCGs upon knockdown of RFX TFs. By using siRNA against RFX1 , RFX2 , and RFX3 , alone or in different combinations, genes were silenced in hTERT-RPE1 cells. Cells were thereafter starved for 24 h to induce ciliogenesis, and expression levels of DYX1C1 , DCDC2 , and KIAA0319 were measured by using qRT-PCR. C ) Fold-change difference in expression levels of RFX1 , RFX2 , and RFX3 upon siRNA silencing. qRT-PCR data are summarized by using the ΔΔC t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem . Significance of the post hoc tests after ANOVA is presented as *** P ≤ 0.001, ** P ≤ 0.01, * P ≤ 0.05 after multiple correction of simultaneous comparisons.
    Figure Legend Snippet: Knockdown of RFX1 , RFX2 , and RFX3 affect the expression of DYX1C1 and DCDC2 but not KIAA0319 in hTERT-RPE1 cells. A ) Binding of RFX1 and RFX2 to the X-box motifs present in DYX1C1 and DCDC2 promoters. Biotinylated probes spanning the X-box motifs were incubated with nuclear extracts from serum-starved hTERT-RPE1 cells with or without antibodies (ab) against RFX1, RFX2, and RFX3. Supershifts for both probes were detected for RFX1 and RFX2 antibodies (white arrowheads). One representative experiment of 3 is shown. B ) Fold-change differences in the expression of DCGs upon knockdown of RFX TFs. By using siRNA against RFX1 , RFX2 , and RFX3 , alone or in different combinations, genes were silenced in hTERT-RPE1 cells. Cells were thereafter starved for 24 h to induce ciliogenesis, and expression levels of DYX1C1 , DCDC2 , and KIAA0319 were measured by using qRT-PCR. C ) Fold-change difference in expression levels of RFX1 , RFX2 , and RFX3 upon siRNA silencing. qRT-PCR data are summarized by using the ΔΔC t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem . Significance of the post hoc tests after ANOVA is presented as *** P ≤ 0.001, ** P ≤ 0.01, * P ≤ 0.05 after multiple correction of simultaneous comparisons.

    Techniques Used: Expressing, Binding Assay, Incubation, Quantitative RT-PCR

    The promoters of DYX1C1 , DCDC2 , and KIAA0319 contain functional X-box promoter motifs. A ) Location of putative X-box promoter motifs upstream of DYX1C1 , DCDC2 , and KIAA0319 identified in the bioinformatics screen. X-box sequence logos on the basis of human, mouse, dog, cow, and cat sequence alignments are shown above 3 well-conserved motifs. B ) Luciferase expression assays: pGL3 basic vector containing promoter sequences of DYX1C1 , DCDC2 , and KIAA0319 (containing WT or mutated X-box motifs) were transfected into starved hTERT-RPE1 and SH-SY5Y cells under normal growth conditions. Luciferase expression was measured and data are shown as relative ratio to the WT construct. Data are displayed as means ± sem. * P
    Figure Legend Snippet: The promoters of DYX1C1 , DCDC2 , and KIAA0319 contain functional X-box promoter motifs. A ) Location of putative X-box promoter motifs upstream of DYX1C1 , DCDC2 , and KIAA0319 identified in the bioinformatics screen. X-box sequence logos on the basis of human, mouse, dog, cow, and cat sequence alignments are shown above 3 well-conserved motifs. B ) Luciferase expression assays: pGL3 basic vector containing promoter sequences of DYX1C1 , DCDC2 , and KIAA0319 (containing WT or mutated X-box motifs) were transfected into starved hTERT-RPE1 and SH-SY5Y cells under normal growth conditions. Luciferase expression was measured and data are shown as relative ratio to the WT construct. Data are displayed as means ± sem. * P

    Techniques Used: Functional Assay, Sequencing, Luciferase, Expressing, Plasmid Preparation, Transfection, Construct

    Induction of ciliogenesis in hTERT-RPE1 cells affects the expression levels of DCGs, RFX TF genes, and ciliogenesis/cell-cycle marker genes. hTERT-RPE1 cells were starved for 6, 12, and 24 h to induce ciliogenesis. Fold-change of difference for each time point compared with 0 h is shown for DYX1C1 ( A ), DCDC2 ( B ), KIAA0319 ( C ), RFX1 ( D ), RFX2 ( E ), RFX3 ( F ), TUBA1A (tubulin α1a) ( G ), IFT57 (intraflagellar transport 57) ( H ), and CDK1 (cyclin-dependent kinase 1) ( I ). qRT-PCR data are summarized by using the ΔΔ C t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem .
    Figure Legend Snippet: Induction of ciliogenesis in hTERT-RPE1 cells affects the expression levels of DCGs, RFX TF genes, and ciliogenesis/cell-cycle marker genes. hTERT-RPE1 cells were starved for 6, 12, and 24 h to induce ciliogenesis. Fold-change of difference for each time point compared with 0 h is shown for DYX1C1 ( A ), DCDC2 ( B ), KIAA0319 ( C ), RFX1 ( D ), RFX2 ( E ), RFX3 ( F ), TUBA1A (tubulin α1a) ( G ), IFT57 (intraflagellar transport 57) ( H ), and CDK1 (cyclin-dependent kinase 1) ( I ). qRT-PCR data are summarized by using the ΔΔ C t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem .

    Techniques Used: Expressing, Marker, Quantitative RT-PCR

    Subcellular localization of endogenous DYX1C1 ( A ) and DCDC2 ( B ) in hTERT-RPE1 cells. hTERT-RPE1 cells were grown to 80% confluence, serum starved for 24 h to induce ciliogenesis, then fixed and stained for DYX1C1, DCDC2, acetylated α-tubulin (cilia marker), or γ-tubulin (centrosome marker). Nuclei are stained with DRAQ5. Scale bars, 20 µm, 2 µm (insets).
    Figure Legend Snippet: Subcellular localization of endogenous DYX1C1 ( A ) and DCDC2 ( B ) in hTERT-RPE1 cells. hTERT-RPE1 cells were grown to 80% confluence, serum starved for 24 h to induce ciliogenesis, then fixed and stained for DYX1C1, DCDC2, acetylated α-tubulin (cilia marker), or γ-tubulin (centrosome marker). Nuclei are stained with DRAQ5. Scale bars, 20 µm, 2 µm (insets).

    Techniques Used: Staining, Marker

    2) Product Images from "aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer"

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-12-79

    Distribution of DYX1C1 mRNA expression stratified by progesterone receptor status and lymph node involvement . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by microarray in the Uppsala cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive lymph node metastasis and negative lymph node metastasis. The expression of DYX1C1 is significantly higher in tumors of lymph node-positive patients. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive and negative periglandular growth. The expression of DYX1C1 is significantly higher in patients with periglandular growth. Note that the y-axis is inverted, a lower dCT value indicates higher expression.
    Figure Legend Snippet: Distribution of DYX1C1 mRNA expression stratified by progesterone receptor status and lymph node involvement . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by microarray in the Uppsala cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive lymph node metastasis and negative lymph node metastasis. The expression of DYX1C1 is significantly higher in tumors of lymph node-positive patients. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive and negative periglandular growth. The expression of DYX1C1 is significantly higher in patients with periglandular growth. Note that the y-axis is inverted, a lower dCT value indicates higher expression.

    Techniques Used: Expressing, Quantitative RT-PCR, Microarray

    Kaplan-Meier plot of Overall Survival for DYX1C1 expression . Overall survival from the time of primary breast cancer diagnosis to death or censoring contrasting the DYX1C1 expression in primary tumor with a threshold greater or equal to 1 as scored by the Allred method classified as positive DYX1C1 expression with negative DYX1C1 expression. The number of patients at risk is shown.
    Figure Legend Snippet: Kaplan-Meier plot of Overall Survival for DYX1C1 expression . Overall survival from the time of primary breast cancer diagnosis to death or censoring contrasting the DYX1C1 expression in primary tumor with a threshold greater or equal to 1 as scored by the Allred method classified as positive DYX1C1 expression with negative DYX1C1 expression. The number of patients at risk is shown.

    Techniques Used: Expressing

    Distribution of DYX1C1 mRNA expression stratified by ERα status . (A) Fold change of DYX1C1 mRNA when comparing the expression between ERα-positive and -negative tumors in CHARES. GAPDH was used for normalization. The bars indicate 1 standard deviation. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between ERα-positive and ERα-negative tumors. The expression of DYX1C1 is significantly higher in ERα-positive tumors (note that the y-axis is inverted in CAHRES, were a lower dCT value indicates a higher expression). (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors.
    Figure Legend Snippet: Distribution of DYX1C1 mRNA expression stratified by ERα status . (A) Fold change of DYX1C1 mRNA when comparing the expression between ERα-positive and -negative tumors in CHARES. GAPDH was used for normalization. The bars indicate 1 standard deviation. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between ERα-positive and ERα-negative tumors. The expression of DYX1C1 is significantly higher in ERα-positive tumors (note that the y-axis is inverted in CAHRES, were a lower dCT value indicates a higher expression). (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors.

    Techniques Used: Expressing, Standard Deviation, Quantitative RT-PCR, Microarray

    Analysis of DYX1C1 mRNA expression among tumor subtype and Elston grade . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the luminal A subtype. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the tumors without classable subtype. (C) Shows the distribution of DYX1C1 between the Elston grades in the Uppsala cohort. The expression was lowest in tumors graded 3. (D) Shows the distribution of DYX1C1 between the Elston grades in the Stockholm cohort. The expression was lowest in tumors graded 3.
    Figure Legend Snippet: Analysis of DYX1C1 mRNA expression among tumor subtype and Elston grade . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the luminal A subtype. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the tumors without classable subtype. (C) Shows the distribution of DYX1C1 between the Elston grades in the Uppsala cohort. The expression was lowest in tumors graded 3. (D) Shows the distribution of DYX1C1 between the Elston grades in the Stockholm cohort. The expression was lowest in tumors graded 3.

    Techniques Used: Expressing, Microarray

    Photomicrograph of immunohistochemical staining with antibodies against DYX1C1 . (A) Patient graded as positively expressing DYX1C1. Almost all of the cancer cells express DYX1C1, the stromal tissue is not stained. (B) Higher magnification of the same patient as in A, staining is cytoplasmic. (C) Patient graded as negative for DYX1C1 expression. (D) Tissue from healthy donor displaying normal mammary tissue, DYX1C1 expression is seen in the epithelial cells.
    Figure Legend Snippet: Photomicrograph of immunohistochemical staining with antibodies against DYX1C1 . (A) Patient graded as positively expressing DYX1C1. Almost all of the cancer cells express DYX1C1, the stromal tissue is not stained. (B) Higher magnification of the same patient as in A, staining is cytoplasmic. (C) Patient graded as negative for DYX1C1 expression. (D) Tissue from healthy donor displaying normal mammary tissue, DYX1C1 expression is seen in the epithelial cells.

    Techniques Used: Immunohistochemistry, Staining, Expressing

    3) Product Images from "The Aromatase Gene CYP19A1: Several Genetic and Functional Lines of Evidence Supporting a Role in Reading, Speech and Language"

    Article Title: The Aromatase Gene CYP19A1: Several Genetic and Functional Lines of Evidence Supporting a Role in Reading, Speech and Language

    Journal: Behavior Genetics

    doi: 10.1007/s10519-012-9532-3

    The CYP19A1 locus on 15q21.2. a An overall map of chromosome 15q shows the relative positions of CYP19A1 , DYX1C1 and the linkage peaks in different studies of dyslexia ( solid lines ) and SSD ( double lines ). b CYP19A1 gene organization, including coding exons ( vertical bars ), promoter regions ( arrowheads ), and the translocation t(2;15)(p12;q21) breakpoint ( slash ). The brain-specific exon/promoter I.f is highlighted with a thicker arrowhead . The gene is located on the reverse strand and therefore is drawn from right (5′) to left (3′). c An evolutionary comparison of the CYP19A1 genomic sequence across four species (dog, mouse, opossum and frog) shows the highest conservation for the brain-specific exon/promoter I.f. The 20 SNPs genotyped in this study are positioned along the gene on the lowest part of the evolutionary sequence comparison. The two SNPs flanking I.f and used in EMSA experiments are indicated by thick red arrows . Colored stars under SNPs are indicating a significantly associated QT to the corresponding marker. In the OH, US, SSD cohort, association to QTs such as phonological processing, oral motor skills and language, is marked with blue , green and yellow stars , respectively. Red stars indicate association to reading measures detected in the GA, US, DYS cohort. d Haplotypes associated with dyslexia as a categorical trait in three of the cohorts and the respective LD structures
    Figure Legend Snippet: The CYP19A1 locus on 15q21.2. a An overall map of chromosome 15q shows the relative positions of CYP19A1 , DYX1C1 and the linkage peaks in different studies of dyslexia ( solid lines ) and SSD ( double lines ). b CYP19A1 gene organization, including coding exons ( vertical bars ), promoter regions ( arrowheads ), and the translocation t(2;15)(p12;q21) breakpoint ( slash ). The brain-specific exon/promoter I.f is highlighted with a thicker arrowhead . The gene is located on the reverse strand and therefore is drawn from right (5′) to left (3′). c An evolutionary comparison of the CYP19A1 genomic sequence across four species (dog, mouse, opossum and frog) shows the highest conservation for the brain-specific exon/promoter I.f. The 20 SNPs genotyped in this study are positioned along the gene on the lowest part of the evolutionary sequence comparison. The two SNPs flanking I.f and used in EMSA experiments are indicated by thick red arrows . Colored stars under SNPs are indicating a significantly associated QT to the corresponding marker. In the OH, US, SSD cohort, association to QTs such as phonological processing, oral motor skills and language, is marked with blue , green and yellow stars , respectively. Red stars indicate association to reading measures detected in the GA, US, DYS cohort. d Haplotypes associated with dyslexia as a categorical trait in three of the cohorts and the respective LD structures

    Techniques Used: Translocation Assay, Sequencing, Marker

    Correlation of CYP19A1 ( y -axis) mRNA expression to four dyslexia genes ( ROBO1 , DYX1C1 , DCDC2 , and KIAA0319 ; x -axis, respectively) in different regions of adult human brain. X - and y -axes are in arbitrary log 2 units. For clarity, the scales are not shown. 1 thalamus; 2 hypothalamus; 3 paracentral gyrus; 4 hippocampus; 5 temporal cortex; 6 frontal cortex; 7 parietal cortex; 8 occipital cortex; 9 postcentral gyrus; 10 whole brain
    Figure Legend Snippet: Correlation of CYP19A1 ( y -axis) mRNA expression to four dyslexia genes ( ROBO1 , DYX1C1 , DCDC2 , and KIAA0319 ; x -axis, respectively) in different regions of adult human brain. X - and y -axes are in arbitrary log 2 units. For clarity, the scales are not shown. 1 thalamus; 2 hypothalamus; 3 paracentral gyrus; 4 hippocampus; 5 temporal cortex; 6 frontal cortex; 7 parietal cortex; 8 occipital cortex; 9 postcentral gyrus; 10 whole brain

    Techniques Used: Expressing

    Related Articles

    Expressing:

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer
    Article Snippet: The quantitative reverse transcriptase PCR (qRT-PCR) was performed in triplicates on the 7500 Fast Real-Time PCR system using TaqMan probes according to standard protocols (Applied Biosystems, Carlsbad, CA, USA). .. DYX1C1 expression was examined by TaqMan assay (Hs00370049_m1) and GAPDH TaqMan assay (Hs99999905_m1) was used for normalization (Applied Biosystems). ..

    Article Title: The Aromatase Gene CYP19A1: Several Genetic and Functional Lines of Evidence Supporting a Role in Reading, Speech and Language
    Article Snippet: Transcription factor binding sites for both alleles of each SNP were predicted by TESS ( www.cbil.upenn.edu/cgi-bin/tess/tess ). .. Expression analysis Ready-made TaqMan gene expression assays for CYP19A1 (Hs00240671_m1), DYX1C1 (Hs00370049_m1), DCDC2 (Hs00393203_m1), KIAA0319 (Hs00207788_m1), ROBO1 (Hs00268049_m1), MRPL19 (Hs00608519_m1), C2ORF3 (Hs00162632_m1), and 18S rRNA (4319413E) were purchased from Applied Biosystems. .. We assayed expression levels for these genes in total RNA from nine different regions of adult human brain: thalamus, hypothalamus, frontal-, occipital-, parietal-, temporal cortex (cat. Nos.

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs
    Article Snippet: Quantitative real-time PCR cDNA was synthesized with SuperScript III First-Strand Synthesis SuperMix kit (11752-250; Thermo Fisher Scientific) by using 500 ng RNA. .. Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA). .. The following SYBR Green primers were used: RFX1: forward, 5′-CAGACGAGCGTGCAGGCCAA-3′; RFX1: reverse, 5′-TGGCCACCTTTGCTGCCTGG-3′; RFX3: forward, 5′-TGGCGATTGAGACGCTGCAAA-3′; RFX3: reverse, 5′-TGGGAAGGCTCACTCCTTCTGCT-3′; HPRT: forward, 5′-TCAGGCAGTATAATCCAAAGATGGT -3′; HPRT: reverse, 5′-AGTCTGGCTTATATCCAACACTTCG-3′.

    TaqMan Assay:

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer
    Article Snippet: The quantitative reverse transcriptase PCR (qRT-PCR) was performed in triplicates on the 7500 Fast Real-Time PCR system using TaqMan probes according to standard protocols (Applied Biosystems, Carlsbad, CA, USA). .. DYX1C1 expression was examined by TaqMan assay (Hs00370049_m1) and GAPDH TaqMan assay (Hs99999905_m1) was used for normalization (Applied Biosystems). ..

    Real-time Polymerase Chain Reaction:

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs
    Article Snippet: Quantitative real-time PCR cDNA was synthesized with SuperScript III First-Strand Synthesis SuperMix kit (11752-250; Thermo Fisher Scientific) by using 500 ng RNA. .. Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA). .. The following SYBR Green primers were used: RFX1: forward, 5′-CAGACGAGCGTGCAGGCCAA-3′; RFX1: reverse, 5′-TGGCCACCTTTGCTGCCTGG-3′; RFX3: forward, 5′-TGGCGATTGAGACGCTGCAAA-3′; RFX3: reverse, 5′-TGGGAAGGCTCACTCCTTCTGCT-3′; HPRT: forward, 5′-TCAGGCAGTATAATCCAAAGATGGT -3′; HPRT: reverse, 5′-AGTCTGGCTTATATCCAACACTTCG-3′.

    Quantitative RT-PCR:

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs
    Article Snippet: Quantitative real-time PCR cDNA was synthesized with SuperScript III First-Strand Synthesis SuperMix kit (11752-250; Thermo Fisher Scientific) by using 500 ng RNA. .. Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA). .. The following SYBR Green primers were used: RFX1: forward, 5′-CAGACGAGCGTGCAGGCCAA-3′; RFX1: reverse, 5′-TGGCCACCTTTGCTGCCTGG-3′; RFX3: forward, 5′-TGGCGATTGAGACGCTGCAAA-3′; RFX3: reverse, 5′-TGGGAAGGCTCACTCCTTCTGCT-3′; HPRT: forward, 5′-TCAGGCAGTATAATCCAAAGATGGT -3′; HPRT: reverse, 5′-AGTCTGGCTTATATCCAACACTTCG-3′.

    Polymerase Chain Reaction:

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs
    Article Snippet: Quantitative real-time PCR cDNA was synthesized with SuperScript III First-Strand Synthesis SuperMix kit (11752-250; Thermo Fisher Scientific) by using 500 ng RNA. .. Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA). .. The following SYBR Green primers were used: RFX1: forward, 5′-CAGACGAGCGTGCAGGCCAA-3′; RFX1: reverse, 5′-TGGCCACCTTTGCTGCCTGG-3′; RFX3: forward, 5′-TGGCGATTGAGACGCTGCAAA-3′; RFX3: reverse, 5′-TGGGAAGGCTCACTCCTTCTGCT-3′; HPRT: forward, 5′-TCAGGCAGTATAATCCAAAGATGGT -3′; HPRT: reverse, 5′-AGTCTGGCTTATATCCAACACTTCG-3′.

    SYBR Green Assay:

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs
    Article Snippet: Quantitative real-time PCR cDNA was synthesized with SuperScript III First-Strand Synthesis SuperMix kit (11752-250; Thermo Fisher Scientific) by using 500 ng RNA. .. Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA). .. The following SYBR Green primers were used: RFX1: forward, 5′-CAGACGAGCGTGCAGGCCAA-3′; RFX1: reverse, 5′-TGGCCACCTTTGCTGCCTGG-3′; RFX3: forward, 5′-TGGCGATTGAGACGCTGCAAA-3′; RFX3: reverse, 5′-TGGGAAGGCTCACTCCTTCTGCT-3′; HPRT: forward, 5′-TCAGGCAGTATAATCCAAAGATGGT -3′; HPRT: reverse, 5′-AGTCTGGCTTATATCCAACACTTCG-3′.

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    Thermo Fisher gene exp dyx1c1 ccpg1 hs00370049 m1
    Knockdown of RFX1 , RFX2 , and RFX3 affect the expression of <t>DYX1C1</t> and DCDC2 but not KIAA0319 in hTERT-RPE1 cells. A ) Binding of RFX1 and RFX2 to the X-box motifs present in DYX1C1 and DCDC2 promoters. Biotinylated probes spanning the X-box motifs were incubated with nuclear extracts from serum-starved hTERT-RPE1 cells with or without antibodies (ab) against RFX1, RFX2, and RFX3. Supershifts for both probes were detected for RFX1 and RFX2 antibodies (white arrowheads). One representative experiment of 3 is shown. B ) Fold-change differences in the expression of DCGs upon knockdown of RFX TFs. By using siRNA against RFX1 , RFX2 , and RFX3 , alone or in different combinations, genes were silenced in hTERT-RPE1 cells. Cells were thereafter starved for 24 h to induce ciliogenesis, and expression levels of DYX1C1 , DCDC2 , and KIAA0319 were measured by using qRT-PCR. C ) Fold-change difference in expression levels of RFX1 , RFX2 , and RFX3 upon siRNA silencing. qRT-PCR data are summarized by using the ΔΔC t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem . Significance of the post hoc tests after ANOVA is presented as *** P ≤ 0.001, ** P ≤ 0.01, * P ≤ 0.05 after multiple correction of simultaneous comparisons.
    Gene Exp Dyx1c1 Ccpg1 Hs00370049 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher gene exp gapdh hs02758991 g1
    Time course expression pattern of ciliary genes. a Venn-diagram of all upregulated genes day 0 vs day 35 and all “Syscilia” ciliary genes detected at day 0 or 35. b Gene set enrichment analysis (GSEA) of “Syscilia” ciliary genes in all detected 11,180 genes. FDR false discovery rate, ES enrichment score. c RNA-seq time course progression plot of the ciliopathy-related genes IFT57 , <t>BBS2</t> , TMEM231, TCTN2 . d qRT-PCR showing upregulation of the dyslexia and ciliopathy-related genes IFT57 , BBS2 , TMEM231, TCTN2 during neuronal differentiation. e Correlation plots of log 2 fold change in RNA-seq vs. log 2 fold change in <t>RT-qPCR.</t> r denotes Pearson correlation coefficient. c , d Mean ± SEM are displayed. c , d , e red: Experiment 1, blue: Experiment 2. Norm. normalized, rel. relative
    Gene Exp Gapdh Hs02758991 G1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gene exp gapdh hs02758991 g1/product/Thermo Fisher
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    Image Search Results


    Knockdown of RFX1 , RFX2 , and RFX3 affect the expression of DYX1C1 and DCDC2 but not KIAA0319 in hTERT-RPE1 cells. A ) Binding of RFX1 and RFX2 to the X-box motifs present in DYX1C1 and DCDC2 promoters. Biotinylated probes spanning the X-box motifs were incubated with nuclear extracts from serum-starved hTERT-RPE1 cells with or without antibodies (ab) against RFX1, RFX2, and RFX3. Supershifts for both probes were detected for RFX1 and RFX2 antibodies (white arrowheads). One representative experiment of 3 is shown. B ) Fold-change differences in the expression of DCGs upon knockdown of RFX TFs. By using siRNA against RFX1 , RFX2 , and RFX3 , alone or in different combinations, genes were silenced in hTERT-RPE1 cells. Cells were thereafter starved for 24 h to induce ciliogenesis, and expression levels of DYX1C1 , DCDC2 , and KIAA0319 were measured by using qRT-PCR. C ) Fold-change difference in expression levels of RFX1 , RFX2 , and RFX3 upon siRNA silencing. qRT-PCR data are summarized by using the ΔΔC t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem . Significance of the post hoc tests after ANOVA is presented as *** P ≤ 0.001, ** P ≤ 0.01, * P ≤ 0.05 after multiple correction of simultaneous comparisons.

    Journal: The FASEB Journal

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs

    doi: 10.1096/fj.201500124RR

    Figure Lengend Snippet: Knockdown of RFX1 , RFX2 , and RFX3 affect the expression of DYX1C1 and DCDC2 but not KIAA0319 in hTERT-RPE1 cells. A ) Binding of RFX1 and RFX2 to the X-box motifs present in DYX1C1 and DCDC2 promoters. Biotinylated probes spanning the X-box motifs were incubated with nuclear extracts from serum-starved hTERT-RPE1 cells with or without antibodies (ab) against RFX1, RFX2, and RFX3. Supershifts for both probes were detected for RFX1 and RFX2 antibodies (white arrowheads). One representative experiment of 3 is shown. B ) Fold-change differences in the expression of DCGs upon knockdown of RFX TFs. By using siRNA against RFX1 , RFX2 , and RFX3 , alone or in different combinations, genes were silenced in hTERT-RPE1 cells. Cells were thereafter starved for 24 h to induce ciliogenesis, and expression levels of DYX1C1 , DCDC2 , and KIAA0319 were measured by using qRT-PCR. C ) Fold-change difference in expression levels of RFX1 , RFX2 , and RFX3 upon siRNA silencing. qRT-PCR data are summarized by using the ΔΔC t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem . Significance of the post hoc tests after ANOVA is presented as *** P ≤ 0.001, ** P ≤ 0.01, * P ≤ 0.05 after multiple correction of simultaneous comparisons.

    Article Snippet: Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA).

    Techniques: Expressing, Binding Assay, Incubation, Quantitative RT-PCR

    The promoters of DYX1C1 , DCDC2 , and KIAA0319 contain functional X-box promoter motifs. A ) Location of putative X-box promoter motifs upstream of DYX1C1 , DCDC2 , and KIAA0319 identified in the bioinformatics screen. X-box sequence logos on the basis of human, mouse, dog, cow, and cat sequence alignments are shown above 3 well-conserved motifs. B ) Luciferase expression assays: pGL3 basic vector containing promoter sequences of DYX1C1 , DCDC2 , and KIAA0319 (containing WT or mutated X-box motifs) were transfected into starved hTERT-RPE1 and SH-SY5Y cells under normal growth conditions. Luciferase expression was measured and data are shown as relative ratio to the WT construct. Data are displayed as means ± sem. * P

    Journal: The FASEB Journal

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs

    doi: 10.1096/fj.201500124RR

    Figure Lengend Snippet: The promoters of DYX1C1 , DCDC2 , and KIAA0319 contain functional X-box promoter motifs. A ) Location of putative X-box promoter motifs upstream of DYX1C1 , DCDC2 , and KIAA0319 identified in the bioinformatics screen. X-box sequence logos on the basis of human, mouse, dog, cow, and cat sequence alignments are shown above 3 well-conserved motifs. B ) Luciferase expression assays: pGL3 basic vector containing promoter sequences of DYX1C1 , DCDC2 , and KIAA0319 (containing WT or mutated X-box motifs) were transfected into starved hTERT-RPE1 and SH-SY5Y cells under normal growth conditions. Luciferase expression was measured and data are shown as relative ratio to the WT construct. Data are displayed as means ± sem. * P

    Article Snippet: Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA).

    Techniques: Functional Assay, Sequencing, Luciferase, Expressing, Plasmid Preparation, Transfection, Construct

    Induction of ciliogenesis in hTERT-RPE1 cells affects the expression levels of DCGs, RFX TF genes, and ciliogenesis/cell-cycle marker genes. hTERT-RPE1 cells were starved for 6, 12, and 24 h to induce ciliogenesis. Fold-change of difference for each time point compared with 0 h is shown for DYX1C1 ( A ), DCDC2 ( B ), KIAA0319 ( C ), RFX1 ( D ), RFX2 ( E ), RFX3 ( F ), TUBA1A (tubulin α1a) ( G ), IFT57 (intraflagellar transport 57) ( H ), and CDK1 (cyclin-dependent kinase 1) ( I ). qRT-PCR data are summarized by using the ΔΔ C t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem .

    Journal: The FASEB Journal

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs

    doi: 10.1096/fj.201500124RR

    Figure Lengend Snippet: Induction of ciliogenesis in hTERT-RPE1 cells affects the expression levels of DCGs, RFX TF genes, and ciliogenesis/cell-cycle marker genes. hTERT-RPE1 cells were starved for 6, 12, and 24 h to induce ciliogenesis. Fold-change of difference for each time point compared with 0 h is shown for DYX1C1 ( A ), DCDC2 ( B ), KIAA0319 ( C ), RFX1 ( D ), RFX2 ( E ), RFX3 ( F ), TUBA1A (tubulin α1a) ( G ), IFT57 (intraflagellar transport 57) ( H ), and CDK1 (cyclin-dependent kinase 1) ( I ). qRT-PCR data are summarized by using the ΔΔ C t method as displayed as mean fold-change (2 −ΔΔ Ct or −2 ΔΔ Ct ) ± sem .

    Article Snippet: Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA).

    Techniques: Expressing, Marker, Quantitative RT-PCR

    Subcellular localization of endogenous DYX1C1 ( A ) and DCDC2 ( B ) in hTERT-RPE1 cells. hTERT-RPE1 cells were grown to 80% confluence, serum starved for 24 h to induce ciliogenesis, then fixed and stained for DYX1C1, DCDC2, acetylated α-tubulin (cilia marker), or γ-tubulin (centrosome marker). Nuclei are stained with DRAQ5. Scale bars, 20 µm, 2 µm (insets).

    Journal: The FASEB Journal

    Article Title: Ciliary dyslexia candidate genes DYX1C1 andDCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs

    doi: 10.1096/fj.201500124RR

    Figure Lengend Snippet: Subcellular localization of endogenous DYX1C1 ( A ) and DCDC2 ( B ) in hTERT-RPE1 cells. hTERT-RPE1 cells were grown to 80% confluence, serum starved for 24 h to induce ciliogenesis, then fixed and stained for DYX1C1, DCDC2, acetylated α-tubulin (cilia marker), or γ-tubulin (centrosome marker). Nuclei are stained with DRAQ5. Scale bars, 20 µm, 2 µm (insets).

    Article Snippet: Quantitative real-time PCR (qRT-PCR) was analyzed with cDNA diluted 1:5 using TaqMan expression assays and TaqMan fast Universal PCR Master Mix [4352042; Thermo Fisher Scientific;DYX1C1 : Hs00370049_m1; DCDC2 : Hs00393203_m1;KIAA0319 : Hs00207788_m1; HPRT 1 (hypoxanthine phosphoribosyltransferase 1): Hs02800695_m1; CDK1 (cyclin-dependent kinase 1): Hs00938777_m1; TUBA1A (tubulin α1a): Hs00362387_m1; RFX2 : 01100925_m1] or using SYBR green primers for RFX1 , RFX3 , and HPRT1 (10 µM) and the Fast SYBR Green Master Mix (4385612; Applied Biosystems, Foster City, CA, USA).

    Techniques: Staining, Marker

    Distribution of DYX1C1 mRNA expression stratified by progesterone receptor status and lymph node involvement . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by microarray in the Uppsala cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive lymph node metastasis and negative lymph node metastasis. The expression of DYX1C1 is significantly higher in tumors of lymph node-positive patients. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive and negative periglandular growth. The expression of DYX1C1 is significantly higher in patients with periglandular growth. Note that the y-axis is inverted, a lower dCT value indicates higher expression.

    Journal: BMC Cancer

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer

    doi: 10.1186/1471-2407-12-79

    Figure Lengend Snippet: Distribution of DYX1C1 mRNA expression stratified by progesterone receptor status and lymph node involvement . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by microarray in the Uppsala cohort between PR-positive and PR-negative tumors. The expression of DYX1C1 is significantly higher in PR-positive tumors. (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive lymph node metastasis and negative lymph node metastasis. The expression of DYX1C1 is significantly higher in tumors of lymph node-positive patients. Note that the y-axis is inverted, a lower dCT value indicates higher expression. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between patients with positive and negative periglandular growth. The expression of DYX1C1 is significantly higher in patients with periglandular growth. Note that the y-axis is inverted, a lower dCT value indicates higher expression.

    Article Snippet: DYX1C1 expression was examined by TaqMan assay (Hs00370049_m1) and GAPDH TaqMan assay (Hs99999905_m1) was used for normalization (Applied Biosystems).

    Techniques: Expressing, Quantitative RT-PCR, Microarray

    Kaplan-Meier plot of Overall Survival for DYX1C1 expression . Overall survival from the time of primary breast cancer diagnosis to death or censoring contrasting the DYX1C1 expression in primary tumor with a threshold greater or equal to 1 as scored by the Allred method classified as positive DYX1C1 expression with negative DYX1C1 expression. The number of patients at risk is shown.

    Journal: BMC Cancer

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer

    doi: 10.1186/1471-2407-12-79

    Figure Lengend Snippet: Kaplan-Meier plot of Overall Survival for DYX1C1 expression . Overall survival from the time of primary breast cancer diagnosis to death or censoring contrasting the DYX1C1 expression in primary tumor with a threshold greater or equal to 1 as scored by the Allred method classified as positive DYX1C1 expression with negative DYX1C1 expression. The number of patients at risk is shown.

    Article Snippet: DYX1C1 expression was examined by TaqMan assay (Hs00370049_m1) and GAPDH TaqMan assay (Hs99999905_m1) was used for normalization (Applied Biosystems).

    Techniques: Expressing

    Distribution of DYX1C1 mRNA expression stratified by ERα status . (A) Fold change of DYX1C1 mRNA when comparing the expression between ERα-positive and -negative tumors in CHARES. GAPDH was used for normalization. The bars indicate 1 standard deviation. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between ERα-positive and ERα-negative tumors. The expression of DYX1C1 is significantly higher in ERα-positive tumors (note that the y-axis is inverted in CAHRES, were a lower dCT value indicates a higher expression). (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors.

    Journal: BMC Cancer

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer

    doi: 10.1186/1471-2407-12-79

    Figure Lengend Snippet: Distribution of DYX1C1 mRNA expression stratified by ERα status . (A) Fold change of DYX1C1 mRNA when comparing the expression between ERα-positive and -negative tumors in CHARES. GAPDH was used for normalization. The bars indicate 1 standard deviation. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by qRT-PCR in the CAHRES cohort between ERα-positive and ERα-negative tumors. The expression of DYX1C1 is significantly higher in ERα-positive tumors (note that the y-axis is inverted in CAHRES, were a lower dCT value indicates a higher expression). (C) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors. (D) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between ERα-positive and ERα-negative tumors. The expression is significantly higher in ERα-positive tumors.

    Article Snippet: DYX1C1 expression was examined by TaqMan assay (Hs00370049_m1) and GAPDH TaqMan assay (Hs99999905_m1) was used for normalization (Applied Biosystems).

    Techniques: Expressing, Standard Deviation, Quantitative RT-PCR, Microarray

    Analysis of DYX1C1 mRNA expression among tumor subtype and Elston grade . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the luminal A subtype. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the tumors without classable subtype. (C) Shows the distribution of DYX1C1 between the Elston grades in the Uppsala cohort. The expression was lowest in tumors graded 3. (D) Shows the distribution of DYX1C1 between the Elston grades in the Stockholm cohort. The expression was lowest in tumors graded 3.

    Journal: BMC Cancer

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer

    doi: 10.1186/1471-2407-12-79

    Figure Lengend Snippet: Analysis of DYX1C1 mRNA expression among tumor subtype and Elston grade . (A) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Uppsala cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the luminal A subtype. (B) Boxplot of the distribution of DYX1C1 mRNA expression examined by Affymetrix microarray in the Stockholm cohort between the different breast cancer subtypes. Lowest median expression is seen in the basal subtype, whereas the highest is seen in the tumors without classable subtype. (C) Shows the distribution of DYX1C1 between the Elston grades in the Uppsala cohort. The expression was lowest in tumors graded 3. (D) Shows the distribution of DYX1C1 between the Elston grades in the Stockholm cohort. The expression was lowest in tumors graded 3.

    Article Snippet: DYX1C1 expression was examined by TaqMan assay (Hs00370049_m1) and GAPDH TaqMan assay (Hs99999905_m1) was used for normalization (Applied Biosystems).

    Techniques: Expressing, Microarray

    Photomicrograph of immunohistochemical staining with antibodies against DYX1C1 . (A) Patient graded as positively expressing DYX1C1. Almost all of the cancer cells express DYX1C1, the stromal tissue is not stained. (B) Higher magnification of the same patient as in A, staining is cytoplasmic. (C) Patient graded as negative for DYX1C1 expression. (D) Tissue from healthy donor displaying normal mammary tissue, DYX1C1 expression is seen in the epithelial cells.

    Journal: BMC Cancer

    Article Title: aThe dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer

    doi: 10.1186/1471-2407-12-79

    Figure Lengend Snippet: Photomicrograph of immunohistochemical staining with antibodies against DYX1C1 . (A) Patient graded as positively expressing DYX1C1. Almost all of the cancer cells express DYX1C1, the stromal tissue is not stained. (B) Higher magnification of the same patient as in A, staining is cytoplasmic. (C) Patient graded as negative for DYX1C1 expression. (D) Tissue from healthy donor displaying normal mammary tissue, DYX1C1 expression is seen in the epithelial cells.

    Article Snippet: DYX1C1 expression was examined by TaqMan assay (Hs00370049_m1) and GAPDH TaqMan assay (Hs99999905_m1) was used for normalization (Applied Biosystems).

    Techniques: Immunohistochemistry, Staining, Expressing

    The CYP19A1 locus on 15q21.2. a An overall map of chromosome 15q shows the relative positions of CYP19A1 , DYX1C1 and the linkage peaks in different studies of dyslexia ( solid lines ) and SSD ( double lines ). b CYP19A1 gene organization, including coding exons ( vertical bars ), promoter regions ( arrowheads ), and the translocation t(2;15)(p12;q21) breakpoint ( slash ). The brain-specific exon/promoter I.f is highlighted with a thicker arrowhead . The gene is located on the reverse strand and therefore is drawn from right (5′) to left (3′). c An evolutionary comparison of the CYP19A1 genomic sequence across four species (dog, mouse, opossum and frog) shows the highest conservation for the brain-specific exon/promoter I.f. The 20 SNPs genotyped in this study are positioned along the gene on the lowest part of the evolutionary sequence comparison. The two SNPs flanking I.f and used in EMSA experiments are indicated by thick red arrows . Colored stars under SNPs are indicating a significantly associated QT to the corresponding marker. In the OH, US, SSD cohort, association to QTs such as phonological processing, oral motor skills and language, is marked with blue , green and yellow stars , respectively. Red stars indicate association to reading measures detected in the GA, US, DYS cohort. d Haplotypes associated with dyslexia as a categorical trait in three of the cohorts and the respective LD structures

    Journal: Behavior Genetics

    Article Title: The Aromatase Gene CYP19A1: Several Genetic and Functional Lines of Evidence Supporting a Role in Reading, Speech and Language

    doi: 10.1007/s10519-012-9532-3

    Figure Lengend Snippet: The CYP19A1 locus on 15q21.2. a An overall map of chromosome 15q shows the relative positions of CYP19A1 , DYX1C1 and the linkage peaks in different studies of dyslexia ( solid lines ) and SSD ( double lines ). b CYP19A1 gene organization, including coding exons ( vertical bars ), promoter regions ( arrowheads ), and the translocation t(2;15)(p12;q21) breakpoint ( slash ). The brain-specific exon/promoter I.f is highlighted with a thicker arrowhead . The gene is located on the reverse strand and therefore is drawn from right (5′) to left (3′). c An evolutionary comparison of the CYP19A1 genomic sequence across four species (dog, mouse, opossum and frog) shows the highest conservation for the brain-specific exon/promoter I.f. The 20 SNPs genotyped in this study are positioned along the gene on the lowest part of the evolutionary sequence comparison. The two SNPs flanking I.f and used in EMSA experiments are indicated by thick red arrows . Colored stars under SNPs are indicating a significantly associated QT to the corresponding marker. In the OH, US, SSD cohort, association to QTs such as phonological processing, oral motor skills and language, is marked with blue , green and yellow stars , respectively. Red stars indicate association to reading measures detected in the GA, US, DYS cohort. d Haplotypes associated with dyslexia as a categorical trait in three of the cohorts and the respective LD structures

    Article Snippet: Expression analysis Ready-made TaqMan gene expression assays for CYP19A1 (Hs00240671_m1), DYX1C1 (Hs00370049_m1), DCDC2 (Hs00393203_m1), KIAA0319 (Hs00207788_m1), ROBO1 (Hs00268049_m1), MRPL19 (Hs00608519_m1), C2ORF3 (Hs00162632_m1), and 18S rRNA (4319413E) were purchased from Applied Biosystems.

    Techniques: Translocation Assay, Sequencing, Marker

    Correlation of CYP19A1 ( y -axis) mRNA expression to four dyslexia genes ( ROBO1 , DYX1C1 , DCDC2 , and KIAA0319 ; x -axis, respectively) in different regions of adult human brain. X - and y -axes are in arbitrary log 2 units. For clarity, the scales are not shown. 1 thalamus; 2 hypothalamus; 3 paracentral gyrus; 4 hippocampus; 5 temporal cortex; 6 frontal cortex; 7 parietal cortex; 8 occipital cortex; 9 postcentral gyrus; 10 whole brain

    Journal: Behavior Genetics

    Article Title: The Aromatase Gene CYP19A1: Several Genetic and Functional Lines of Evidence Supporting a Role in Reading, Speech and Language

    doi: 10.1007/s10519-012-9532-3

    Figure Lengend Snippet: Correlation of CYP19A1 ( y -axis) mRNA expression to four dyslexia genes ( ROBO1 , DYX1C1 , DCDC2 , and KIAA0319 ; x -axis, respectively) in different regions of adult human brain. X - and y -axes are in arbitrary log 2 units. For clarity, the scales are not shown. 1 thalamus; 2 hypothalamus; 3 paracentral gyrus; 4 hippocampus; 5 temporal cortex; 6 frontal cortex; 7 parietal cortex; 8 occipital cortex; 9 postcentral gyrus; 10 whole brain

    Article Snippet: Expression analysis Ready-made TaqMan gene expression assays for CYP19A1 (Hs00240671_m1), DYX1C1 (Hs00370049_m1), DCDC2 (Hs00393203_m1), KIAA0319 (Hs00207788_m1), ROBO1 (Hs00268049_m1), MRPL19 (Hs00608519_m1), C2ORF3 (Hs00162632_m1), and 18S rRNA (4319413E) were purchased from Applied Biosystems.

    Techniques: Expressing

    Time course expression pattern of ciliary genes. a Venn-diagram of all upregulated genes day 0 vs day 35 and all “Syscilia” ciliary genes detected at day 0 or 35. b Gene set enrichment analysis (GSEA) of “Syscilia” ciliary genes in all detected 11,180 genes. FDR false discovery rate, ES enrichment score. c RNA-seq time course progression plot of the ciliopathy-related genes IFT57 , BBS2 , TMEM231, TCTN2 . d qRT-PCR showing upregulation of the dyslexia and ciliopathy-related genes IFT57 , BBS2 , TMEM231, TCTN2 during neuronal differentiation. e Correlation plots of log 2 fold change in RNA-seq vs. log 2 fold change in RT-qPCR. r denotes Pearson correlation coefficient. c , d Mean ± SEM are displayed. c , d , e red: Experiment 1, blue: Experiment 2. Norm. normalized, rel. relative

    Journal: Molecular Neurobiology

    Article Title: Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation

    doi: 10.1007/s12035-020-01905-6

    Figure Lengend Snippet: Time course expression pattern of ciliary genes. a Venn-diagram of all upregulated genes day 0 vs day 35 and all “Syscilia” ciliary genes detected at day 0 or 35. b Gene set enrichment analysis (GSEA) of “Syscilia” ciliary genes in all detected 11,180 genes. FDR false discovery rate, ES enrichment score. c RNA-seq time course progression plot of the ciliopathy-related genes IFT57 , BBS2 , TMEM231, TCTN2 . d qRT-PCR showing upregulation of the dyslexia and ciliopathy-related genes IFT57 , BBS2 , TMEM231, TCTN2 during neuronal differentiation. e Correlation plots of log 2 fold change in RNA-seq vs. log 2 fold change in RT-qPCR. r denotes Pearson correlation coefficient. c , d Mean ± SEM are displayed. c , d , e red: Experiment 1, blue: Experiment 2. Norm. normalized, rel. relative

    Article Snippet: The reagents used for RT-qPCR were TaqMan fast Universal PCR Master Mix (Thermo Fisher Scientific) and Taqman probes (BBS2: Hs00230400_m1; DCDC2: Hs00393203_m1; DYX1C1: Hs00370049_m1; GAPDH: Hs02758991_g1; IFT57 (ESRRBL1): Hs00215973_m1; KIAA0319: Hs00207788_m1; TCTN2: Hs00430714_m1; TMEM231: Hs00226008_m1; TUBA1A: Hs00362387_m1) or FastStart Universal SYBR Green Master (Roche Diagnostics, Mannheim, Germany) and SYBR green primers (DCX_F: TTG CTG GCT GAC CTG ACG CG; DCX_R: GCT GCT AGC CAA GGA CTG GGG; GAPDH_F: CCA CAT CGC TCA GAC ACC AT; GAPDH_R: GCG CCC AAT ACG ACC AAA T; MAP2_F: AGG CAG AGA CAC AGG TGC TT; MAP2_R: GGG TTT GCT CCT AGG GTT TC; TUBB3_F: CCT ACT GCA TCG ACA ACG AG; TUBB3_R: CGA TAC CAG GTG GTT GAG GT).

    Techniques: Expressing, RNA Sequencing Assay, Quantitative RT-PCR