dna microarrays Search Results


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  • 99
    Millipore dna microarrays chip chip
    Dna Microarrays Chip Chip, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Zymo Research chip dna
    Binding of Bcl11b to regulatory regions in the Thpok gene. a <t>DNA</t> pull-down assay showing in vitro Bcl11b binding to wild-type (Wt) Thpok silencer ( Sth ) core sequences, but not efficiently to mutant (Mut.) sequences. One representative of two experiments. b Co-immune precipitation assay showing interaction of Bcl11b with Runx1. One representative of two experiments. c Flow cytometry showing an increase of CD8 + T cells de-repressing Thpok-GFP upon reduction of Bcl11b dosage in Runx mutant mice. One representative of two independent experiments. d Bcl11b ChIP-seq tracks at the Thpok , Thpok gfp:ΔTESPE , and Sfpi1 genes in total thymocytes along with Runx ChIP-seq (GSE90794) tracks at the Thpok gene ( top ) for reference. Gene structure, transcriptional orientation and conservations in mammals (Cons.) in the Thpok gene are indicated. Positions of Thpok silencer ( Sth ), two enhancers ( TE and PE ), distal P1-promoter ( P1 ) and proximal enhancer ( PE ) in the Thpok gene, and upstream regulatory element ( URE ) in the Sfpi1 gene are indicated as arrowheads . e Co-occupancy by Runx at Bcl11b-bound genome regions. Runx recognition site (5′-ACCPuCA-3′) was listed among the top two common sequences for Bcl11b-bound regions. f ChIP-PCR assay for binding of Runx, Bcl11b, and ThPOK to Wt and Runx site mutated (RSM) Sth regions in CD4 + T cells from Thpok +/gfp:241-401RM mice. Lanes 1, 2, and 3 are input, control IgG and antibody-against the indicated transcription factor, respectively. One representative of two independent experiments. g <t>ChIP-qPCR</t> analyses showing binding of Runx and Bcl11b to the Sth and PE in CD4 + (white bars) and CD8 + (gray bars) T cells. Combined data from three independent ChIP experiments is shown. ** P
    Chip Dna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 316 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher dna microarray chips
    Expression of a subset of 'trophoblast stem cell-associated' genes . A) Representative northern blot analysis of 'trophoblast stem cell-associated' genes identified by <t>DNA</t> <t>microarray</t> analysis. B) qRT-PCR analysis of 'trophoblast stem cell-associated' genes identified by DNA microarray analysis. See Table 1 for a list and description of the mRNAs investigated. Rcho-1 trophoblast stem cells were cultured under stem (S) or differentiating (D) conditions. Rat placental samples were also included in the analysis and are from gestation d11.5 trophoblast and d18.5 junctional zone. Student's t -tests (*P
    Dna Microarray Chips, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Agilent technologies oligonucleotide microarray chips
    Technical validation of <t>microarray</t> data by quantitative RT-PCR (QRT-PCR). Average Log2 expression of relative mRNA copy numbers derived from three replicate microarray experiments and QRT-PCR of migratory (rim) over stationary (core) glioma cells (error bars = SD). Concordance between directionality of differential regulation between migratory and stationary cells for microarray and QRT-PCR data is displayed in parentheses (CYR61 = cystein rich 61, CTGF = connective tissue growth factor, RRAS2 = related RAS viral oncogene homolog 2, RhoA = ras homolog gene family member A, PCAF = p300/CBP-associated factor, ITM2B = integral membrane protein 2B, ZNF436 = zinc finger protein 436, MADH1 = mothers against decapentaplegic homolog 1 ( A ). Expression pattern of migratory ( B ) and stationary signatures ( C ) in comprehensive glioma expression data set (NB = normal brain, LGA = low grade astrocytoma, AA = anaplastic astrocytoma, GBM = glioblastoma multiforme). Bar indicates genes significantly (P
    Oligonucleotide Microarray Chips, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Agilent technologies dna microarray chip
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Dna Microarray Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 79 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher dna array chip
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Dna Array Chip, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligonucleotide based dna chip microarrays
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Oligonucleotide Based Dna Chip Microarrays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Arbor Biosciences dna microarrays chips
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Dna Microarrays Chips, supplied by Arbor Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    MicroFluidic Systems microarray dna chips
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Microarray Dna Chips, supplied by MicroFluidic Systems, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    ATUM chip dna
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Chip Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad dna chips
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Dna Chips, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 96/100, based on 118 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rae230a gene chip dna microarrays
    Confirmation of <t>DNA</t> <t>microarray</t> gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).
    Rae230a Gene Chip Dna Microarrays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    BioMed Diagnostics Inc dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Dna Chip, supplied by BioMed Diagnostics Inc, used in various techniques. Bioz Stars score: 86/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dna microarrays chip chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Dna Microarrays Chip Chip, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies dna microarrays chip chip chip chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Dna Microarrays Chip Chip Chip Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies microarray dna chip analysis
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Microarray Dna Chip Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher microarray dna chip analysis
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Microarray Dna Chip Analysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Greiner Bio utilises dna microarray chips
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Utilises Dna Microarray Chips, supplied by Greiner Bio, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MWG-Biotech dna microarray chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Dna Microarray Chip, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 85/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BioCore hpv dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Hpv Dna Chip, supplied by BioCore, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Agilent technologies 2x400k dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    2x400k Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    PerkinElmer hs dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Hs Dna Chip, supplied by PerkinElmer, used in various techniques. Bioz Stars score: 89/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies fetal dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Fetal Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 96/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad experion dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Experion Dna Chip, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 90/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Agilent technologies 4x44k chip on chip whole genome dna microarray platform
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    4x44k Chip On Chip Whole Genome Dna Microarray Platform, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Yokogawa Electric dna chip reader
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Dna Chip Reader, supplied by Yokogawa Electric, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies bioanalyser dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Bioanalyser Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies hs dna chip
    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows <t>DNA</t> methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean <t>RNA</t> level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.
    Hs Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 231 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher chip based dna microarray analysis
    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows <t>DNA</t> methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean <t>RNA</t> level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.
    Chip Based Dna Microarray Analysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/chip based dna microarray analysis/product/Thermo Fisher
    Average 90 stars, based on 19 article reviews
    Price from $9.99 to $1999.99
    chip based dna microarray analysis - by Bioz Stars, 2020-04
    90/100 stars
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    85
    Thermo Fisher mgu74av2 dna chips
    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows <t>DNA</t> methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean <t>RNA</t> level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.
    Mgu74av2 Dna Chips, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mgu74av2 dna chips/product/Thermo Fisher
    Average 85 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    mgu74av2 dna chips - by Bioz Stars, 2020-04
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    Image Search Results


    Binding of Bcl11b to regulatory regions in the Thpok gene. a DNA pull-down assay showing in vitro Bcl11b binding to wild-type (Wt) Thpok silencer ( Sth ) core sequences, but not efficiently to mutant (Mut.) sequences. One representative of two experiments. b Co-immune precipitation assay showing interaction of Bcl11b with Runx1. One representative of two experiments. c Flow cytometry showing an increase of CD8 + T cells de-repressing Thpok-GFP upon reduction of Bcl11b dosage in Runx mutant mice. One representative of two independent experiments. d Bcl11b ChIP-seq tracks at the Thpok , Thpok gfp:ΔTESPE , and Sfpi1 genes in total thymocytes along with Runx ChIP-seq (GSE90794) tracks at the Thpok gene ( top ) for reference. Gene structure, transcriptional orientation and conservations in mammals (Cons.) in the Thpok gene are indicated. Positions of Thpok silencer ( Sth ), two enhancers ( TE and PE ), distal P1-promoter ( P1 ) and proximal enhancer ( PE ) in the Thpok gene, and upstream regulatory element ( URE ) in the Sfpi1 gene are indicated as arrowheads . e Co-occupancy by Runx at Bcl11b-bound genome regions. Runx recognition site (5′-ACCPuCA-3′) was listed among the top two common sequences for Bcl11b-bound regions. f ChIP-PCR assay for binding of Runx, Bcl11b, and ThPOK to Wt and Runx site mutated (RSM) Sth regions in CD4 + T cells from Thpok +/gfp:241-401RM mice. Lanes 1, 2, and 3 are input, control IgG and antibody-against the indicated transcription factor, respectively. One representative of two independent experiments. g ChIP-qPCR analyses showing binding of Runx and Bcl11b to the Sth and PE in CD4 + (white bars) and CD8 + (gray bars) T cells. Combined data from three independent ChIP experiments is shown. ** P

    Journal: Nature Communications

    Article Title: Priming of lineage-specifying genes by Bcl11b is required for lineage choice in post-selection thymocytes

    doi: 10.1038/s41467-017-00768-1

    Figure Lengend Snippet: Binding of Bcl11b to regulatory regions in the Thpok gene. a DNA pull-down assay showing in vitro Bcl11b binding to wild-type (Wt) Thpok silencer ( Sth ) core sequences, but not efficiently to mutant (Mut.) sequences. One representative of two experiments. b Co-immune precipitation assay showing interaction of Bcl11b with Runx1. One representative of two experiments. c Flow cytometry showing an increase of CD8 + T cells de-repressing Thpok-GFP upon reduction of Bcl11b dosage in Runx mutant mice. One representative of two independent experiments. d Bcl11b ChIP-seq tracks at the Thpok , Thpok gfp:ΔTESPE , and Sfpi1 genes in total thymocytes along with Runx ChIP-seq (GSE90794) tracks at the Thpok gene ( top ) for reference. Gene structure, transcriptional orientation and conservations in mammals (Cons.) in the Thpok gene are indicated. Positions of Thpok silencer ( Sth ), two enhancers ( TE and PE ), distal P1-promoter ( P1 ) and proximal enhancer ( PE ) in the Thpok gene, and upstream regulatory element ( URE ) in the Sfpi1 gene are indicated as arrowheads . e Co-occupancy by Runx at Bcl11b-bound genome regions. Runx recognition site (5′-ACCPuCA-3′) was listed among the top two common sequences for Bcl11b-bound regions. f ChIP-PCR assay for binding of Runx, Bcl11b, and ThPOK to Wt and Runx site mutated (RSM) Sth regions in CD4 + T cells from Thpok +/gfp:241-401RM mice. Lanes 1, 2, and 3 are input, control IgG and antibody-against the indicated transcription factor, respectively. One representative of two independent experiments. g ChIP-qPCR analyses showing binding of Runx and Bcl11b to the Sth and PE in CD4 + (white bars) and CD8 + (gray bars) T cells. Combined data from three independent ChIP experiments is shown. ** P

    Article Snippet: DNA was purified by Phenol/Chloroform extraction for ChIP-seq or ChIP DNA Clean and Concentrator kit (ZYMO RESEARCH) for ChIP-qPCR.

    Techniques: Binding Assay, Pull Down Assay, In Vitro, Mutagenesis, Flow Cytometry, Cytometry, Mouse Assay, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Acidosis-driven MondoA transcriptional activity depends on electron transport. ( A and B ) TXNIP protein levels were determine by immunoblotting following a 4 hr HBSS treatment of MEFs in the presence of the indicated inhibitors. Cont; control, Chlor; Chloroquine (25 μM), Mon; monensin (5 μM), Met; metformin (1 mM), FCCP; carbonilcyanide p -triflouromethoxyphenylhydrazone (1 µM), Oligo; oligomycin (1 μM). ( C–E ), TXNIP mRNA levels were determine using RT-qPCR following 4 hr treatments with DMEM Acidic : ( C ) 143B osteosarcoma cells, ( D ) 143Bρ 0 cells, and ( E ) 143Bρ 0 :WT-Cybrid cells complemented with wild type mitochondria. ( F ) Schematic depicting nuclear- and mitochondrial-DNA encoded components of the ETC. ( G ) TXNIP mRNA levels following 4 hr DMEM Acidic treatments of 143Bρ 0 :ΔATP6/ATP8-Cybrid cells expressing empty vector or nuclear encoded, mitochondrial-targeted ATP6 and ATP8. *p

    Journal: eLife

    Article Title: Cellular acidosis triggers human MondoA transcriptional activity by driving mitochondrial ATP production

    doi: 10.7554/eLife.40199

    Figure Lengend Snippet: Acidosis-driven MondoA transcriptional activity depends on electron transport. ( A and B ) TXNIP protein levels were determine by immunoblotting following a 4 hr HBSS treatment of MEFs in the presence of the indicated inhibitors. Cont; control, Chlor; Chloroquine (25 μM), Mon; monensin (5 μM), Met; metformin (1 mM), FCCP; carbonilcyanide p -triflouromethoxyphenylhydrazone (1 µM), Oligo; oligomycin (1 μM). ( C–E ), TXNIP mRNA levels were determine using RT-qPCR following 4 hr treatments with DMEM Acidic : ( C ) 143B osteosarcoma cells, ( D ) 143Bρ 0 cells, and ( E ) 143Bρ 0 :WT-Cybrid cells complemented with wild type mitochondria. ( F ) Schematic depicting nuclear- and mitochondrial-DNA encoded components of the ETC. ( G ) TXNIP mRNA levels following 4 hr DMEM Acidic treatments of 143Bρ 0 :ΔATP6/ATP8-Cybrid cells expressing empty vector or nuclear encoded, mitochondrial-targeted ATP6 and ATP8. *p

    Article Snippet: After reversal of crosslinks and ChIP DNA purification (Zymo Research, D5201), MondoA binding on TXNIP, ARRDC4, KLF10 and TMEM97 were determined by normalizing to input.

    Techniques: Activity Assay, Quantitative RT-PCR, Expressing, Plasmid Preparation

    Biological replicates for ChIP experiments in Figure 5 . ChIP assays were performed with FAMAp:FAMA-MYC in Col ( A ), FAMAp:RBR-MYC in Col ( B ), and FAMAp:RBR-MYC in FAMA LGK plants ( C ) using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated gene promoters or the negative control region, IR1 or RB45 ( Cruz-Ramirez et al., 2012 ) and ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.015

    Journal: eLife

    Article Title: Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module

    doi: 10.7554/eLife.03271

    Figure Lengend Snippet: Biological replicates for ChIP experiments in Figure 5 . ChIP assays were performed with FAMAp:FAMA-MYC in Col ( A ), FAMAp:RBR-MYC in Col ( B ), and FAMAp:RBR-MYC in FAMA LGK plants ( C ) using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated gene promoters or the negative control region, IR1 or RB45 ( Cruz-Ramirez et al., 2012 ) and ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.015

    Article Snippet: ChIPed DNA was purified by the ChIP DNA Clean & Concentrator (Zymo).

    Techniques: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Negative Control

    Dissection of FAMA and RBR binding on stomatal target genes. ( A and D ) Map of the SPCH ( A ) and EPF1 ( D ) loci. Arrow indicates orientation of the gene and the transcription start site. Genome coordinate is indicated above the gene structure. Black bars indicate genomic region probed by ChIP-qPCR assays. Key: U, upstream; P, promoter; D, downstream. ( B , C , E and F ) ChIP assays were performed with FAMAp:FAMA-MYC in fama ( B and E ) and FAMAp:RBR-MYC in Col ( C and F ), using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated genomic regions relative to SPCH ( B and C ) and EPF1 ( E and F ) or the negative control region, RB45 ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.016

    Journal: eLife

    Article Title: Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module

    doi: 10.7554/eLife.03271

    Figure Lengend Snippet: Dissection of FAMA and RBR binding on stomatal target genes. ( A and D ) Map of the SPCH ( A ) and EPF1 ( D ) loci. Arrow indicates orientation of the gene and the transcription start site. Genome coordinate is indicated above the gene structure. Black bars indicate genomic region probed by ChIP-qPCR assays. Key: U, upstream; P, promoter; D, downstream. ( B , C , E and F ) ChIP assays were performed with FAMAp:FAMA-MYC in fama ( B and E ) and FAMAp:RBR-MYC in Col ( C and F ), using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated genomic regions relative to SPCH ( B and C ) and EPF1 ( E and F ) or the negative control region, RB45 ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.016

    Article Snippet: ChIPed DNA was purified by the ChIP DNA Clean & Concentrator (Zymo).

    Techniques: Dissection, Binding Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Negative Control

    SUMOylation facilitates HDAC2-to-ROR-γt binding and inhibits IL-17 expression. a Lysates from cLPLs of WT mice were immunoprecipitated with anti-ROR-γt, anti-HDAC2 antibody, or control IgG antibody and immunoblotted with antibody against ROR-γt or HDAC2. b Transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt were immunoprecipitated with anti-V5 antibody and immunoblot with antibody against V5 or HDAC2. c Binding of HDAC2 to the IL-17 promoter was assessed by ChIP analysis using a DNA-protein complex from cLPLs of WT mice that was immunoprecipitated with anti-ROR-γt, anti-HDAC2, or control IgG antibody. d SUMOylation of ROR-γt facilitates HDAC2 recruitment to the IL-17 promoter. ChIP analysis was conducted using DNA-protein complex from transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt and immunoprecipitated with anti–ROR-γt, anti-HDAC2, or control IgG antibody. e A luciferase assay was performed of lysates from Jurkat T cells transfected with various combinations (below plot) of IL - 17-promoter-driven luciferase plasmid (pGL4-mIL17p), plasmid encoding WT-ROR-γt or K187R-ROR-γt along with either HDAC2-WT or HDAC2-H141A. Results are presented in relative luciferase units (RLU). Data are from one experiment representative of three or more independent experiments with similar results. * p

    Journal: Nature Communications

    Article Title: SUMOylation of ROR-γt inhibits IL-17 expression and inflammation via HDAC2

    doi: 10.1038/s41467-018-06924-5

    Figure Lengend Snippet: SUMOylation facilitates HDAC2-to-ROR-γt binding and inhibits IL-17 expression. a Lysates from cLPLs of WT mice were immunoprecipitated with anti-ROR-γt, anti-HDAC2 antibody, or control IgG antibody and immunoblotted with antibody against ROR-γt or HDAC2. b Transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt were immunoprecipitated with anti-V5 antibody and immunoblot with antibody against V5 or HDAC2. c Binding of HDAC2 to the IL-17 promoter was assessed by ChIP analysis using a DNA-protein complex from cLPLs of WT mice that was immunoprecipitated with anti-ROR-γt, anti-HDAC2, or control IgG antibody. d SUMOylation of ROR-γt facilitates HDAC2 recruitment to the IL-17 promoter. ChIP analysis was conducted using DNA-protein complex from transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt and immunoprecipitated with anti–ROR-γt, anti-HDAC2, or control IgG antibody. e A luciferase assay was performed of lysates from Jurkat T cells transfected with various combinations (below plot) of IL - 17-promoter-driven luciferase plasmid (pGL4-mIL17p), plasmid encoding WT-ROR-γt or K187R-ROR-γt along with either HDAC2-WT or HDAC2-H141A. Results are presented in relative luciferase units (RLU). Data are from one experiment representative of three or more independent experiments with similar results. * p

    Article Snippet: After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was purified using the ChIP DNA Clean kit (Zymo Research, Irvine, CA, USA).

    Techniques: Binding Assay, Expressing, Mouse Assay, Immunoprecipitation, Chromatin Immunoprecipitation, Luciferase, Transfection, Plasmid Preparation

    ITGA6 is a direct HIF transcriptional target gene. a A schematic representation of putative HREs identified in the proximal promoter of ITGA6 that were assessed for HIF-1α and/or HIF-2α recruitment by ChIP assays. b MDA-MB-231 shControl and shHIF1A cells were cultured at hypoxia (0.5 % O 2 ) for 6 h, and chromatin fragments were immunoprecipitated using HIF-1α or HIF-2α antibodies or anti-rabbit IgG (as the non-specific binding control). SYBR Green-based qRT-PCR was conducted on the purified, isolated DNA fragments to determine the site fold enrichment of HIFα recruitment relative to signal detected in the anti-rabbit IgG control per genotype (qRT-PCR values observed for the IgG control were set to 1.0 per genotype). As the positive control, qRT-PCR was also performed using primers flanking a previously validated, functional HRE site in the 3’ EPO enhancer. Each panel shows the mean site fold enrichment ± SEM of technical replicates; data presented are representative of three replicate experiments. c Luciferase reporter assays were used to compare relative luciferase activity between MDA-MB-231 shControl or shHIF1A/shHIF2A cells transiently transfected with a wild type ITGA6 promoter linked to luciferase (ITGA6-Luc; white bars) or a HRE mutant promoter construct [ITGA6 (mutant)-Luc; grey bars] and then cultured at normoxia (Nor) or hypoxia (Hyp). In some cases, a stabilized version of murine HIF-1α was also co-transfected (+HIF1A). The mean ± standard deviation are shown; p

    Journal: Molecular Cancer

    Article Title: ITGA6 is directly regulated by hypoxia-inducible factors and enriches for cancer stem cell activity and invasion in metastatic breast cancer models

    doi: 10.1186/s12943-016-0510-x

    Figure Lengend Snippet: ITGA6 is a direct HIF transcriptional target gene. a A schematic representation of putative HREs identified in the proximal promoter of ITGA6 that were assessed for HIF-1α and/or HIF-2α recruitment by ChIP assays. b MDA-MB-231 shControl and shHIF1A cells were cultured at hypoxia (0.5 % O 2 ) for 6 h, and chromatin fragments were immunoprecipitated using HIF-1α or HIF-2α antibodies or anti-rabbit IgG (as the non-specific binding control). SYBR Green-based qRT-PCR was conducted on the purified, isolated DNA fragments to determine the site fold enrichment of HIFα recruitment relative to signal detected in the anti-rabbit IgG control per genotype (qRT-PCR values observed for the IgG control were set to 1.0 per genotype). As the positive control, qRT-PCR was also performed using primers flanking a previously validated, functional HRE site in the 3’ EPO enhancer. Each panel shows the mean site fold enrichment ± SEM of technical replicates; data presented are representative of three replicate experiments. c Luciferase reporter assays were used to compare relative luciferase activity between MDA-MB-231 shControl or shHIF1A/shHIF2A cells transiently transfected with a wild type ITGA6 promoter linked to luciferase (ITGA6-Luc; white bars) or a HRE mutant promoter construct [ITGA6 (mutant)-Luc; grey bars] and then cultured at normoxia (Nor) or hypoxia (Hyp). In some cases, a stabilized version of murine HIF-1α was also co-transfected (+HIF1A). The mean ± standard deviation are shown; p

    Article Snippet: Reverse crosslinking was accomplished by adding 1 μl of 10 mg/ml RNase and 5 M NaCl to a final concentration of 0.2 M and incubation at 65 °C for 5 h, followed by digestion with Proteinase K at 37 °C for 1 h. Immunoprecipitated DNA was recovered using the ChIP DNA Clean and Concentrator kit (Zymo Research, Irvine, CA). qRT-PCR was performed on all samples using LightCycler 480 SYBR Green master mix.

    Techniques: Chromatin Immunoprecipitation, Multiple Displacement Amplification, Cell Culture, Immunoprecipitation, Binding Assay, SYBR Green Assay, Quantitative RT-PCR, Purification, Isolation, Positive Control, Functional Assay, Luciferase, Activity Assay, Transfection, Mutagenesis, Construct, Standard Deviation

    Expression of a subset of 'trophoblast stem cell-associated' genes . A) Representative northern blot analysis of 'trophoblast stem cell-associated' genes identified by DNA microarray analysis. B) qRT-PCR analysis of 'trophoblast stem cell-associated' genes identified by DNA microarray analysis. See Table 1 for a list and description of the mRNAs investigated. Rcho-1 trophoblast stem cells were cultured under stem (S) or differentiating (D) conditions. Rat placental samples were also included in the analysis and are from gestation d11.5 trophoblast and d18.5 junctional zone. Student's t -tests (*P

    Journal: BMC Developmental Biology

    Article Title: Phosphatidylinositol 3 kinase modulation of trophoblast cell differentiation

    doi: 10.1186/1471-213X-10-97

    Figure Lengend Snippet: Expression of a subset of 'trophoblast stem cell-associated' genes . A) Representative northern blot analysis of 'trophoblast stem cell-associated' genes identified by DNA microarray analysis. B) qRT-PCR analysis of 'trophoblast stem cell-associated' genes identified by DNA microarray analysis. See Table 1 for a list and description of the mRNAs investigated. Rcho-1 trophoblast stem cells were cultured under stem (S) or differentiating (D) conditions. Rat placental samples were also included in the analysis and are from gestation d11.5 trophoblast and d18.5 junctional zone. Student's t -tests (*P

    Article Snippet: DNA microarray Affymetrix 230 2.0 DNA microarray chips (Affymetrix, Santa Clara, CA) were probed with cDNAs generated from Rcho-1 trophoblast cells grown under stem or differentiation conditions with chronic exposure to LY294002 or vehicle.

    Techniques: Expressing, Northern Blot, Microarray, Quantitative RT-PCR, Cell Culture

    Expression of a subset of trophoblast 'differentiation-associated' genes . A) Representative northern blot analysis of trophoblast 'differentiation-associated' genes identified by DNA microarray analysis. B) qRT-PCR analysis of trophoblast 'differentiation-associated' genes identified by DNA microarray analysis. See Table 2 for a list and description of the mRNAs investigated. Rcho-1 trophoblast stem cells were cultured under stem (S) or differentiating (D) conditions. Rat placental samples were also included in the analysis and are from gestation d11.5 trophoblast and d18.5 junctional zone. Student's t -tests (*P

    Journal: BMC Developmental Biology

    Article Title: Phosphatidylinositol 3 kinase modulation of trophoblast cell differentiation

    doi: 10.1186/1471-213X-10-97

    Figure Lengend Snippet: Expression of a subset of trophoblast 'differentiation-associated' genes . A) Representative northern blot analysis of trophoblast 'differentiation-associated' genes identified by DNA microarray analysis. B) qRT-PCR analysis of trophoblast 'differentiation-associated' genes identified by DNA microarray analysis. See Table 2 for a list and description of the mRNAs investigated. Rcho-1 trophoblast stem cells were cultured under stem (S) or differentiating (D) conditions. Rat placental samples were also included in the analysis and are from gestation d11.5 trophoblast and d18.5 junctional zone. Student's t -tests (*P

    Article Snippet: DNA microarray Affymetrix 230 2.0 DNA microarray chips (Affymetrix, Santa Clara, CA) were probed with cDNAs generated from Rcho-1 trophoblast cells grown under stem or differentiation conditions with chronic exposure to LY294002 or vehicle.

    Techniques: Expressing, Northern Blot, Microarray, Quantitative RT-PCR, Cell Culture

    PI3K regulation: Analysis of microarray data and expression of a subset of PI3K regulated genes . A) Scatter graph showing the signal intensity of probe sets. B) Functional analysis of negatively and positively regulated genes by PI3K using Ingenuity Pathway Analysis software. C) Representative northern blot analyses of genes regulated by PI3K originally identified by DNA microarray analysis. D) qRT-PCR analysis of genes regulated by PI3K originally identified by DNA microarray analysis. See Tables 1 and 2 for a list and description of the mRNAs investigated. Rcho-1 trophoblast stem cells were cultured under differentiating conditions with exposure to vehicle (0.1% DMSO; D+V) or LY294002 (10 μM; D+LY). Student's t -tests (*P

    Journal: BMC Developmental Biology

    Article Title: Phosphatidylinositol 3 kinase modulation of trophoblast cell differentiation

    doi: 10.1186/1471-213X-10-97

    Figure Lengend Snippet: PI3K regulation: Analysis of microarray data and expression of a subset of PI3K regulated genes . A) Scatter graph showing the signal intensity of probe sets. B) Functional analysis of negatively and positively regulated genes by PI3K using Ingenuity Pathway Analysis software. C) Representative northern blot analyses of genes regulated by PI3K originally identified by DNA microarray analysis. D) qRT-PCR analysis of genes regulated by PI3K originally identified by DNA microarray analysis. See Tables 1 and 2 for a list and description of the mRNAs investigated. Rcho-1 trophoblast stem cells were cultured under differentiating conditions with exposure to vehicle (0.1% DMSO; D+V) or LY294002 (10 μM; D+LY). Student's t -tests (*P

    Article Snippet: DNA microarray Affymetrix 230 2.0 DNA microarray chips (Affymetrix, Santa Clara, CA) were probed with cDNAs generated from Rcho-1 trophoblast cells grown under stem or differentiation conditions with chronic exposure to LY294002 or vehicle.

    Techniques: Microarray, Expressing, Functional Assay, Software, Northern Blot, Quantitative RT-PCR, Cell Culture

    Derepression of Hmga2 in Bmi1 −/− Ink4a-Arf −/− hematopoietic cells. (A) List of top 10 genes up-regulated in LSK cells and CMPs in the absence of Bmi1. IL-7Rα LSK cells purified from BM of 4-wk-old Ink4a-Arf −/− (DKO) and Bmi1 −/− Ink4a-Arf −/− (TKO) mice and CMPs from recipients’ BM at 4 mo after infusion of DKO and TKO BM cells were subjected to microarray analyses and their profiles were compared. Highlighted genes were further characterized in this study. (B) Quantitative RT-PCR analysis of Hmga2 expression. mRNA levels in each progenitor fraction from the recipients’ BM repopulated by BM cells of the indicated genotype at 4 mo after transplantation were normalized to Hprt1 expression. Expression levels relative to those in the wild-type Flt3 − LSK cells are shown as the mean ± SD for triplicate analyses. The fold change in expression levels between Bmi1 −/− Ink4a-Arf −/− cells and Ink4a-Arf −/− cells is also indicated. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Lethal myelofibrosis induced by Bmi1-deficient hematopoietic cells unveils a tumor suppressor function of the polycomb group genes

    doi: 10.1084/jem.20111709

    Figure Lengend Snippet: Derepression of Hmga2 in Bmi1 −/− Ink4a-Arf −/− hematopoietic cells. (A) List of top 10 genes up-regulated in LSK cells and CMPs in the absence of Bmi1. IL-7Rα LSK cells purified from BM of 4-wk-old Ink4a-Arf −/− (DKO) and Bmi1 −/− Ink4a-Arf −/− (TKO) mice and CMPs from recipients’ BM at 4 mo after infusion of DKO and TKO BM cells were subjected to microarray analyses and their profiles were compared. Highlighted genes were further characterized in this study. (B) Quantitative RT-PCR analysis of Hmga2 expression. mRNA levels in each progenitor fraction from the recipients’ BM repopulated by BM cells of the indicated genotype at 4 mo after transplantation were normalized to Hprt1 expression. Expression levels relative to those in the wild-type Flt3 − LSK cells are shown as the mean ± SD for triplicate analyses. The fold change in expression levels between Bmi1 −/− Ink4a-Arf −/− cells and Ink4a-Arf −/− cells is also indicated. *, P

    Article Snippet: Target cRNA was prepared from the total RNA equivalent to 10,000 cells (IL-7Rα LSK) or 8,000 cells (CMPs) with a two-cycle cDNA synthesis kit and 3′-amplification reagents for IVT labeling (Affymetrix), and then hybridized to a GeneChip Mouse Genome 430 2.0 oligonucleotide microarray (Affymetrix) according to the manufacturer’s instructions.

    Techniques: Purification, Mouse Assay, Microarray, Quantitative RT-PCR, Expressing, Transplantation Assay

    Technical validation of microarray data by quantitative RT-PCR (QRT-PCR). Average Log2 expression of relative mRNA copy numbers derived from three replicate microarray experiments and QRT-PCR of migratory (rim) over stationary (core) glioma cells (error bars = SD). Concordance between directionality of differential regulation between migratory and stationary cells for microarray and QRT-PCR data is displayed in parentheses (CYR61 = cystein rich 61, CTGF = connective tissue growth factor, RRAS2 = related RAS viral oncogene homolog 2, RhoA = ras homolog gene family member A, PCAF = p300/CBP-associated factor, ITM2B = integral membrane protein 2B, ZNF436 = zinc finger protein 436, MADH1 = mothers against decapentaplegic homolog 1 ( A ). Expression pattern of migratory ( B ) and stationary signatures ( C ) in comprehensive glioma expression data set (NB = normal brain, LGA = low grade astrocytoma, AA = anaplastic astrocytoma, GBM = glioblastoma multiforme). Bar indicates genes significantly (P

    Journal: BMC Genomics

    Article Title: Glioma cells on the run - the migratory transcriptome of 10 human glioma cell lines

    doi: 10.1186/1471-2164-9-54

    Figure Lengend Snippet: Technical validation of microarray data by quantitative RT-PCR (QRT-PCR). Average Log2 expression of relative mRNA copy numbers derived from three replicate microarray experiments and QRT-PCR of migratory (rim) over stationary (core) glioma cells (error bars = SD). Concordance between directionality of differential regulation between migratory and stationary cells for microarray and QRT-PCR data is displayed in parentheses (CYR61 = cystein rich 61, CTGF = connective tissue growth factor, RRAS2 = related RAS viral oncogene homolog 2, RhoA = ras homolog gene family member A, PCAF = p300/CBP-associated factor, ITM2B = integral membrane protein 2B, ZNF436 = zinc finger protein 436, MADH1 = mothers against decapentaplegic homolog 1 ( A ). Expression pattern of migratory ( B ) and stationary signatures ( C ) in comprehensive glioma expression data set (NB = normal brain, LGA = low grade astrocytoma, AA = anaplastic astrocytoma, GBM = glioblastoma multiforme). Bar indicates genes significantly (P

    Article Snippet: Microarray processing and quality testing Each Cy5-labeled core and rim sample (three biological replicates) was hybridized against Cy3-labeled universal reference RNA on whole human genome 40 K oligonucleotide microarray chips (Agilent) according to manufacture's protocol [ ].

    Techniques: Microarray, Quantitative RT-PCR, Expressing, Derivative Assay

    Immunohistochemistry of matched glioma core and rim samples as well as normal brain control from a glioma invasion specific tissue microarray (TMA). Staining for CTGF exhibits strong signal in a majority of invasive cells (rim, arrows) compared to stationary cells from tumor core. Normal brain control shows only weak staining; size standard = 200 μm. Median staining intensity for CTGF assessed separately in core and rim cells is represented as bar chart; pie charts represent staining intensity for respective portion of glioma cells separately in core and rim (*, p

    Journal: BMC Genomics

    Article Title: Glioma cells on the run - the migratory transcriptome of 10 human glioma cell lines

    doi: 10.1186/1471-2164-9-54

    Figure Lengend Snippet: Immunohistochemistry of matched glioma core and rim samples as well as normal brain control from a glioma invasion specific tissue microarray (TMA). Staining for CTGF exhibits strong signal in a majority of invasive cells (rim, arrows) compared to stationary cells from tumor core. Normal brain control shows only weak staining; size standard = 200 μm. Median staining intensity for CTGF assessed separately in core and rim cells is represented as bar chart; pie charts represent staining intensity for respective portion of glioma cells separately in core and rim (*, p

    Article Snippet: Microarray processing and quality testing Each Cy5-labeled core and rim sample (three biological replicates) was hybridized against Cy3-labeled universal reference RNA on whole human genome 40 K oligonucleotide microarray chips (Agilent) according to manufacture's protocol [ ].

    Techniques: Immunohistochemistry, Microarray, Staining

    Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Extraction, Chromatin Immunoprecipitation, Electrophoresis, Polymerase Chain Reaction

    Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Purification, Chromatin Immunoprecipitation, Electrophoresis

    Venn diagram indicating the number of differentially expressed genes in medulloblastoma from the comparisons of different microarray systems. A total of 4,596 (1,656 up- and 2,940 downregulated) genes from Agilent microarray system, 12,262 (8,306 up- and 3,956 downregulated) genes from GEO GSE7578, and 14,257 (11,274 up- and 2,983 downregulated) genes from GEO GSE22139 were respectively selected according to their differential expression. Gray regions indicated the genes repeated in different experiments. Only 2,544 genes with consistent expression level differences were determined by comparing the data obtained from Agilent and Affymetrix (GEO GSE7578 and GSE22139) microarrays. GEO, Gene Expression Omnibus; GSE, GEO series.

    Journal: International Journal of Molecular Medicine

    Article Title: Detection of lower levels of SNAP25 using multiple microarray systems and its functional significance in medulloblastoma

    doi: 10.3892/ijmm.2017.2925

    Figure Lengend Snippet: Venn diagram indicating the number of differentially expressed genes in medulloblastoma from the comparisons of different microarray systems. A total of 4,596 (1,656 up- and 2,940 downregulated) genes from Agilent microarray system, 12,262 (8,306 up- and 3,956 downregulated) genes from GEO GSE7578, and 14,257 (11,274 up- and 2,983 downregulated) genes from GEO GSE22139 were respectively selected according to their differential expression. Gray regions indicated the genes repeated in different experiments. Only 2,544 genes with consistent expression level differences were determined by comparing the data obtained from Agilent and Affymetrix (GEO GSE7578 and GSE22139) microarrays. GEO, Gene Expression Omnibus; GSE, GEO series.

    Article Snippet: We identified 4,596 candidates based on their significantly up- ( > 1.50-fold) or downregulated ( < 0.67-fold) expression levels in MB cells using Agilent oligonucleotide microarrays.

    Techniques: Microarray, Expressing

    Confirmation of DNA microarray gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).

    Journal: The Journal of Biological Chemistry

    Article Title: The Ssl2245-Sll1130 Toxin-Antitoxin System Mediates Heat-induced Programmed Cell Death in Synechocystis sp. PCC6803 *

    doi: 10.1074/jbc.M116.748178

    Figure Lengend Snippet: Confirmation of DNA microarray gene expression changes by qRT-PCR. Genes whose expression was up-regulated ( slr7064 , sll7067 , sll7085 , sll7090 , slr7091 , and sll5097 ) and the genes whose expression was down-regulated ( slr0909 , sll1396 , and sll6010 ) due to mutation in Δ sll1130 as well as in Δ ssl2245 cells were selected for qRT-PCR analysis. Black and gray bars represent -fold changes observed by DNA microarray analysis; white and striped bars represent -fold changes observed by qRT-PCR analysis due to the mutation in Δ sll1130 and Δ ssl2245 , respectively. Similar results were obtained in two independent experiments; data are presented as mean ratios ±S.D. ( error bars ).

    Article Snippet: Dye-coupled cDNA was purified using microspin columns and hybridized to the DNA microarray chip according to the manufacturer's recommendations (gene expression hybridization kit, catalog number 5188-5281, Agilent Technologies Inc.).

    Techniques: Microarray, Expressing, Quantitative RT-PCR, Mutagenesis

    The human papillomavirus (HPV) oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a DNA chip scanner

    Journal:

    Article Title: Multinucleation of koilocytes is in fact multilobation and is related to aberration of the G2 checkpoint

    doi: 10.1136/jcp.2004.022152

    Figure Lengend Snippet: The human papillomavirus (HPV) oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a DNA chip scanner

    Article Snippet: After confirmation of 22 HPV genotypes by DNA chip (Biomed Lab Co, Seoul, Korea), we looked at koilocytes from the cervical swab and tissue specimens by three dimensional confocal restoration—we reconstructed stacks of two dimensional images of koilocytes to produce three dimensional images by confocal microscopy.

    Techniques: Microarray, Chromatin Immunoprecipitation

    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows DNA methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean RNA level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.

    Journal: The Journal of Clinical Investigation

    Article Title: Comparative oncogenomics identifies tyrosine kinase FES as a tumor suppressor in melanoma

    doi: 10.1172/JCI91291

    Figure Lengend Snippet: FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows DNA methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean RNA level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.

    Article Snippet: Illumina’s NextSeq library Prep Kit (Illumina) was used to prepare the library from 1000 ng of RNA and the library quality was monitored on an HS DNA chip (Bioanalyzer, Agilent).

    Techniques: Expressing, Methylation, DNA Methylation Assay, Quantitative RT-PCR, Western Blot, Methylation Sequencing, Cell Culture