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  • 93
    Thermo Fisher duplicated
    Duplicated, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher duplication
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    91
    Pacific Biosciences duplication breakpoint
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    Molecular Devices LLC duplicated spots
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    Geno Technology duplicated gels
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    91
    SourceForge net pcr duplication
    CRISPR/Cas9-induced deletion of the Lefty1 and Lefty2 upstream SBSs. ( A ) Characterization of the P19 clones deleted for Lefty1 and Lefty2 upstream SBSs. Three individual clones are shown for each deletion. Fragments were amplified from genomic DNA by <t>PCR</t> using primers flanking the positions of the guide RNAs. Wild type genomic DNA was used as a control. M, 100 bp DNA ladder. ( B ) DNA regions deleted in the individual clones. In all cases the clones are compound heterozygotes. In the case of Lefty2 , the deletions are the same on both alleles of the different clones, but the flanking sequences are not identical. ( C and D ) qPCR for the genes shown in wild type (WT) P19 cells and in the clones deleted for Lefty1 ( C ) and Lefty2 ( D ) upstream SBSs. The cells were either untreated (Untr) or incubated overnight with SB-431542, washed out, then replaced with full media containing Activin for the times shown. Representative experiments are shown (mean ± SD). DOI: <t>http://dx.doi.org/10.7554/eLife.22474.010</t>
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    90
    Leister Technologies segmental duplication
    CRISPR/Cas9-induced deletion of the Lefty1 and Lefty2 upstream SBSs. ( A ) Characterization of the P19 clones deleted for Lefty1 and Lefty2 upstream SBSs. Three individual clones are shown for each deletion. Fragments were amplified from genomic DNA by <t>PCR</t> using primers flanking the positions of the guide RNAs. Wild type genomic DNA was used as a control. M, 100 bp DNA ladder. ( B ) DNA regions deleted in the individual clones. In all cases the clones are compound heterozygotes. In the case of Lefty2 , the deletions are the same on both alleles of the different clones, but the flanking sequences are not identical. ( C and D ) qPCR for the genes shown in wild type (WT) P19 cells and in the clones deleted for Lefty1 ( C ) and Lefty2 ( D ) upstream SBSs. The cells were either untreated (Untr) or incubated overnight with SB-431542, washed out, then replaced with full media containing Activin for the times shown. Representative experiments are shown (mean ± SD). DOI: <t>http://dx.doi.org/10.7554/eLife.22474.010</t>
    Segmental Duplication, supplied by Leister Technologies, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    SourceForge net pcr duplicates
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Pcr Duplicates, supplied by SourceForge net, used in various techniques. Bioz Stars score: 92/100, based on 569 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc duplicate removed illumina
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Duplicate Removed Illumina, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Horizon Discovery sirna duplices
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Sirna Duplices, supplied by Horizon Discovery, 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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    90
    Leister Technologies duplication
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Duplication, supplied by Leister Technologies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    MRC-Holland duplication
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Duplication, supplied by MRC-Holland, used in various techniques. Bioz Stars score: 88/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    V&P Scientific duplication
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Duplication, supplied by V&P Scientific, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Genomed GmbH duplication
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Duplication, supplied by Genomed GmbH, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Santa Cruz Biotechnology duplication
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Duplication, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Mimetics duplics
    Rosetteless splicing and protein levels. ( A ) <t>RT-PCR</t> with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. <t>rosetta</t> cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015
    Duplics, supplied by Mimetics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher duplicate triplicate cfc dishes
    A single <t>hEB</t> cell generates one blast colony with bipotential hematoendothelial capacity. (A) hEB cell dose response. To demonstrate that a single hEB cell has hemangioblastic capacity, the linear correlation of <t>BL-CFC</t> to the number of unfractionated
    Duplicate Triplicate Cfc Dishes, 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
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    85
    Quest Diagnostics 13q34 duplication
    Genomic rearrangement at <t>13q34.</t> The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.
    13q34 Duplication, supplied by Quest Diagnostics, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Covidence de duplicated
    Genomic rearrangement at <t>13q34.</t> The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.
    De Duplicated, supplied by Covidence, used in various techniques. Bioz Stars score: 93/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Microsoft de duplicated
    Genomic rearrangement at <t>13q34.</t> The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.
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    Covidence de duplication
    Genomic rearrangement at <t>13q34.</t> The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.
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    Medicago duplication event
    Genomic rearrangement at <t>13q34.</t> The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.
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    Syntaxin kb duplication
    Genomic rearrangement at <t>13q34.</t> The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.
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    SourceForge net mark duplicate
    Genomic rearrangement at <t>13q34.</t> The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.
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    Image Search Results


    CRISPR/Cas9-induced deletion of the Lefty1 and Lefty2 upstream SBSs. ( A ) Characterization of the P19 clones deleted for Lefty1 and Lefty2 upstream SBSs. Three individual clones are shown for each deletion. Fragments were amplified from genomic DNA by PCR using primers flanking the positions of the guide RNAs. Wild type genomic DNA was used as a control. M, 100 bp DNA ladder. ( B ) DNA regions deleted in the individual clones. In all cases the clones are compound heterozygotes. In the case of Lefty2 , the deletions are the same on both alleles of the different clones, but the flanking sequences are not identical. ( C and D ) qPCR for the genes shown in wild type (WT) P19 cells and in the clones deleted for Lefty1 ( C ) and Lefty2 ( D ) upstream SBSs. The cells were either untreated (Untr) or incubated overnight with SB-431542, washed out, then replaced with full media containing Activin for the times shown. Representative experiments are shown (mean ± SD). DOI: http://dx.doi.org/10.7554/eLife.22474.010

    Journal: eLife

    Article Title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

    doi: 10.7554/eLife.22474

    Figure Lengend Snippet: CRISPR/Cas9-induced deletion of the Lefty1 and Lefty2 upstream SBSs. ( A ) Characterization of the P19 clones deleted for Lefty1 and Lefty2 upstream SBSs. Three individual clones are shown for each deletion. Fragments were amplified from genomic DNA by PCR using primers flanking the positions of the guide RNAs. Wild type genomic DNA was used as a control. M, 100 bp DNA ladder. ( B ) DNA regions deleted in the individual clones. In all cases the clones are compound heterozygotes. In the case of Lefty2 , the deletions are the same on both alleles of the different clones, but the flanking sequences are not identical. ( C and D ) qPCR for the genes shown in wild type (WT) P19 cells and in the clones deleted for Lefty1 ( C ) and Lefty2 ( D ) upstream SBSs. The cells were either untreated (Untr) or incubated overnight with SB-431542, washed out, then replaced with full media containing Activin for the times shown. Representative experiments are shown (mean ± SD). DOI: http://dx.doi.org/10.7554/eLife.22474.010

    Article Snippet: For the Pol II and histone ChIP-seq datasets the alignments were post-processed with picard-tools 1.107 for the removal of reads that could have arisen from PCR duplication ( http://sourceforge.net/projects/picard/ ).

    Techniques: CRISPR, Clone Assay, Amplification, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Incubation

    Relationship between chromatin state and SMAD2 binding strength. ( A ) Hierarchical clustering of average read intensity (Log 2 ) over a 5 kb window surrounding all SMAD2 consensus peak summits for each indicated treatment is shown for H3K27Ac (left panel) and H3K9Ac (right panel). Red line, peaks associated with low overall acetylation; blue line, peaks found in highly acetylated chromatin. ( B – D ) Correlation between normalized SMAD2 read counts and H3 acetylation state. The SMAD2 read counts over consensus peaks in either the ‘low overall acetylation’ (red) or ‘high overall acetylation’ (blue) category were plotted for the three conditions ( B ). The SMAD2 read counts over consensus peaks that were defined as either low H3Ac or high H3Ac in the SB-431542 state were plotted for the 1 hr and 8 hr Activin conditions ( C ). The SMAD2 read counts over subsets of loci selected based on changes in H3Ac enrichment from a low baseline ( D ). In all cases the black bars indicate the mean and 95% confidence interval. n.s., not significant. The p-values are given in the plots. ( E ) ChIP-PCR for H3K4Me1 for the nucleosomes at and flanking the Lefty1 SBS or a control region within the Gapdh coding locus. A representative experiment is shown (means ± SD). DOI: http://dx.doi.org/10.7554/eLife.22474.019 10.7554/eLife.22474.020 Average read intensity over a 5 kb window surrounding all SMAD2 consensus peak summits for H3K27Ac and H3K9Ac. DOI: http://dx.doi.org/10.7554/eLife.22474.020

    Journal: eLife

    Article Title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

    doi: 10.7554/eLife.22474

    Figure Lengend Snippet: Relationship between chromatin state and SMAD2 binding strength. ( A ) Hierarchical clustering of average read intensity (Log 2 ) over a 5 kb window surrounding all SMAD2 consensus peak summits for each indicated treatment is shown for H3K27Ac (left panel) and H3K9Ac (right panel). Red line, peaks associated with low overall acetylation; blue line, peaks found in highly acetylated chromatin. ( B – D ) Correlation between normalized SMAD2 read counts and H3 acetylation state. The SMAD2 read counts over consensus peaks in either the ‘low overall acetylation’ (red) or ‘high overall acetylation’ (blue) category were plotted for the three conditions ( B ). The SMAD2 read counts over consensus peaks that were defined as either low H3Ac or high H3Ac in the SB-431542 state were plotted for the 1 hr and 8 hr Activin conditions ( C ). The SMAD2 read counts over subsets of loci selected based on changes in H3Ac enrichment from a low baseline ( D ). In all cases the black bars indicate the mean and 95% confidence interval. n.s., not significant. The p-values are given in the plots. ( E ) ChIP-PCR for H3K4Me1 for the nucleosomes at and flanking the Lefty1 SBS or a control region within the Gapdh coding locus. A representative experiment is shown (means ± SD). DOI: http://dx.doi.org/10.7554/eLife.22474.019 10.7554/eLife.22474.020 Average read intensity over a 5 kb window surrounding all SMAD2 consensus peak summits for H3K27Ac and H3K9Ac. DOI: http://dx.doi.org/10.7554/eLife.22474.020

    Article Snippet: For the Pol II and histone ChIP-seq datasets the alignments were post-processed with picard-tools 1.107 for the removal of reads that could have arisen from PCR duplication ( http://sourceforge.net/projects/picard/ ).

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Polymerase Chain Reaction

    IGV browser displays of genes and associated peaks showing changes in chromatin landscape. IGV browser displays over the Pmepa1, Trh and Smad7 loci. Displayed are ChIP-seq tracks for SMAD2, H3K9Ac, H3K27Ac and total histone H3 in P19 cells which were treated as indicated. MACS-called peaks for SMAD2 are also shown, and the regions amplified in ChIP-PCR ( Figure 5—figure supplement 1 ) are denoted below each panel. DOI: http://dx.doi.org/10.7554/eLife.22474.017

    Journal: eLife

    Article Title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

    doi: 10.7554/eLife.22474

    Figure Lengend Snippet: IGV browser displays of genes and associated peaks showing changes in chromatin landscape. IGV browser displays over the Pmepa1, Trh and Smad7 loci. Displayed are ChIP-seq tracks for SMAD2, H3K9Ac, H3K27Ac and total histone H3 in P19 cells which were treated as indicated. MACS-called peaks for SMAD2 are also shown, and the regions amplified in ChIP-PCR ( Figure 5—figure supplement 1 ) are denoted below each panel. DOI: http://dx.doi.org/10.7554/eLife.22474.017

    Article Snippet: For the Pol II and histone ChIP-seq datasets the alignments were post-processed with picard-tools 1.107 for the removal of reads that could have arisen from PCR duplication ( http://sourceforge.net/projects/picard/ ).

    Techniques: Chromatin Immunoprecipitation, Magnetic Cell Separation, Amplification, Polymerase Chain Reaction

    The role of FOXH1 in SMAD2-mediated transcription. ( A ) For experiment shown in Figure 7A , where gene expression following siRNA-mediated knockdown of Foxh1 or Pou5f1 was assessed, qPCR was performed on the untreated samples to determine expression levels of Pou5f1 and Foxh1 itself, as quantified relative to endogenous Gapdh . Means ± SEM of three independent experiments performed in duplicate are shown. NT, non-targeting. ( B ) Lysates were collected from wild type P19 cells or P19 cells stably expressing MYC-tagged FOXH1, treated for the indicated times with either 20 ng/ml Activin and/or 10 µM SB-431542. Shown are Western blots for MYC, pSMAD2 and MCM6 (loading). Note that expression of MYC-FOXH1 does not alter the kinetics of pSMAD2 induction. ( C ) qPCR for Foxh1 was performed on samples collected from either wild type P19 cells or P19 cells stably expressing MYC-tagged FOXH1 as in ( B ), treated as indicated. Shown are expression levels of Foxh1 determined relative to Gapdh . Note that MYC-FOXH1 is expressed at roughly endogenous levels. A representative experiment (means ± SD) is shown. ( D ) ChIP-PCR for MYC-FOXH1 at the indicated SBSs and negative control (Neg ctrl) region using the P19 cells stably expressing MYC-tagged FOXH1 as in ( B ) in the conditions shown. A representative experiment (means ± SD) is shown. ( E ) qPCR for Foxh1 performed on non-targeting (NT) control or Foxh1 siRNA-transfected cells used for the experiments shown in Figure 7D–F to show the efficiency of knockdown. Values were normalized to endogenous Gapdh . A representative experiment (means ± SD) is shown. ( F ) A control H3K27Ac ChIP-PCR on the Gapdh TSS from the samples used in Figure 7E . A representative experiment (means ± SD) is shown. DOI: http://dx.doi.org/10.7554/eLife.22474.024

    Journal: eLife

    Article Title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

    doi: 10.7554/eLife.22474

    Figure Lengend Snippet: The role of FOXH1 in SMAD2-mediated transcription. ( A ) For experiment shown in Figure 7A , where gene expression following siRNA-mediated knockdown of Foxh1 or Pou5f1 was assessed, qPCR was performed on the untreated samples to determine expression levels of Pou5f1 and Foxh1 itself, as quantified relative to endogenous Gapdh . Means ± SEM of three independent experiments performed in duplicate are shown. NT, non-targeting. ( B ) Lysates were collected from wild type P19 cells or P19 cells stably expressing MYC-tagged FOXH1, treated for the indicated times with either 20 ng/ml Activin and/or 10 µM SB-431542. Shown are Western blots for MYC, pSMAD2 and MCM6 (loading). Note that expression of MYC-FOXH1 does not alter the kinetics of pSMAD2 induction. ( C ) qPCR for Foxh1 was performed on samples collected from either wild type P19 cells or P19 cells stably expressing MYC-tagged FOXH1 as in ( B ), treated as indicated. Shown are expression levels of Foxh1 determined relative to Gapdh . Note that MYC-FOXH1 is expressed at roughly endogenous levels. A representative experiment (means ± SD) is shown. ( D ) ChIP-PCR for MYC-FOXH1 at the indicated SBSs and negative control (Neg ctrl) region using the P19 cells stably expressing MYC-tagged FOXH1 as in ( B ) in the conditions shown. A representative experiment (means ± SD) is shown. ( E ) qPCR for Foxh1 performed on non-targeting (NT) control or Foxh1 siRNA-transfected cells used for the experiments shown in Figure 7D–F to show the efficiency of knockdown. Values were normalized to endogenous Gapdh . A representative experiment (means ± SD) is shown. ( F ) A control H3K27Ac ChIP-PCR on the Gapdh TSS from the samples used in Figure 7E . A representative experiment (means ± SD) is shown. DOI: http://dx.doi.org/10.7554/eLife.22474.024

    Article Snippet: For the Pol II and histone ChIP-seq datasets the alignments were post-processed with picard-tools 1.107 for the removal of reads that could have arisen from PCR duplication ( http://sourceforge.net/projects/picard/ ).

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Stable Transfection, Western Blot, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Negative Control, Transfection

    Characterization of SMAD2 and Pol II binding in response to Activin signaling. ( A and B ) IGV browser displays over the Lefty1/Lefty2 locus ( A ) or Pmepa1 locus ( B ) for the 2 replicates of the SMAD2 ChIP-seq experiment to show consistency between duplicates. The tracks and MACS-called peaks for SMAD2 are shown. The conditions are as in Figure 2A . SMAD2 binding sites (SBSs) that are subsequently analyzed in the paper are indicated with a red line. ( C ) SMAD2 ChIP-PCR validations performed in the same treatment conditions as the ChIP-seq experiment for selected SBSs found near target genes ( Lefty1, Tdgf1, Nodal ). The negative control (Neg ctrl) region primers amplify an intergenic region on Chromosome 5 devoid of detectable SMAD2 binding. A representative experiment is shown (mean ± SD). ( D ) ChIP-PCR validations of Pol II Ser2P and Ser5P on the Lefty1 gene using the same treatment conditions as the ChIP-seq experiment, showing enrichment at the SBS, TSS and TTS sites relative to a negative control (Neg ctrl) region and the Gapdh TSS. A representative experiment is shown (mean ± SD). DOI: http://dx.doi.org/10.7554/eLife.22474.009

    Journal: eLife

    Article Title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

    doi: 10.7554/eLife.22474

    Figure Lengend Snippet: Characterization of SMAD2 and Pol II binding in response to Activin signaling. ( A and B ) IGV browser displays over the Lefty1/Lefty2 locus ( A ) or Pmepa1 locus ( B ) for the 2 replicates of the SMAD2 ChIP-seq experiment to show consistency between duplicates. The tracks and MACS-called peaks for SMAD2 are shown. The conditions are as in Figure 2A . SMAD2 binding sites (SBSs) that are subsequently analyzed in the paper are indicated with a red line. ( C ) SMAD2 ChIP-PCR validations performed in the same treatment conditions as the ChIP-seq experiment for selected SBSs found near target genes ( Lefty1, Tdgf1, Nodal ). The negative control (Neg ctrl) region primers amplify an intergenic region on Chromosome 5 devoid of detectable SMAD2 binding. A representative experiment is shown (mean ± SD). ( D ) ChIP-PCR validations of Pol II Ser2P and Ser5P on the Lefty1 gene using the same treatment conditions as the ChIP-seq experiment, showing enrichment at the SBS, TSS and TTS sites relative to a negative control (Neg ctrl) region and the Gapdh TSS. A representative experiment is shown (mean ± SD). DOI: http://dx.doi.org/10.7554/eLife.22474.009

    Article Snippet: For the Pol II and histone ChIP-seq datasets the alignments were post-processed with picard-tools 1.107 for the removal of reads that could have arisen from PCR duplication ( http://sourceforge.net/projects/picard/ ).

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Magnetic Cell Separation, Polymerase Chain Reaction, Negative Control

    Rosetteless splicing and protein levels. ( A ) RT-PCR with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. rosetta cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015

    Journal: eLife

    Article Title: The rosetteless gene controls development in the choanoflagellate S. rosetta

    doi: 10.7554/eLife.04070

    Figure Lengend Snippet: Rosetteless splicing and protein levels. ( A ) RT-PCR with a primer bridging the exon 7/8 boundary of rtls paired with a primer in exon 12, amplified the wild-type rtls splice isoform from wild-type and rtls l1 cDNA. This was in contrast with the diverse alternative rtls splice isoforms amplified from Rosetteless cells when RT-PCR was performed with a primer bridging the exon 5/6 junction and a primer in exon 12 ( Figure 5D ). ( B ) Purified, recombinant protein corresponding to the anti-Rtls epitope has a predicted size of approximately 38 kDa (arrowhead). The purity of 100 ng of recombinant protein was analyzed by silver stain (left) and by western blot with anti-Rtls (right) on two separate 4–12% gradient gels. ( C ) Raw data showing the validation of anti-Rtls on dot blots of wild-type cell lysates. Pre-incubation of anti-Rtls with the recombinant Rtls epitope competes away the staining, demonstrating that the majority of the signal is specific to the Rtls protein. Three replicate samples are shown. ( D ) Raw dot blot data showing levels of Rtls in wild-type (WT) or Rosetteless mutant ( rtls l1 ) cultures with or without inoculation with A. machipongonensis ( Alg .). Each spot is normalized for total S. rosetta cell number. DOI: http://dx.doi.org/10.7554/eLife.04070.015

    Article Snippet: Trimmed reads were mapped to the S. rosetta reference genome ( ) using Burrows-Wheeler Aligner , and we removed PCR duplicates with Picard ( http://picard.sourceforge.net ).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Amplification, Purification, Recombinant, Silver Staining, Western Blot, Incubation, Staining, Dot Blot, Mutagenesis

    A single hEB cell generates one blast colony with bipotential hematoendothelial capacity. (A) hEB cell dose response. To demonstrate that a single hEB cell has hemangioblastic capacity, the linear correlation of BL-CFC to the number of unfractionated

    Journal: Blood

    Article Title: Expression of angiotensin-converting enzyme (CD143) identifies and regulates primitive hemangioblasts derived from human pluripotent stem cells

    doi: 10.1182/blood-2008-03-144766

    Figure Lengend Snippet: A single hEB cell generates one blast colony with bipotential hematoendothelial capacity. (A) hEB cell dose response. To demonstrate that a single hEB cell has hemangioblastic capacity, the linear correlation of BL-CFC to the number of unfractionated

    Article Snippet: Aliquots of viable hEB cells (which ranged between 40% and 75%) were enumerated by fluorescence-activated cell sorting (FACS) analysis before plating. hEB cells were plated (1.0-2.0 × 105 viable cells/mL) in duplicate/triplicate CFC dishes (NUNC A/S, Roskilde, Denmark), and assayed in humidified chambers for the presence of hematopoietic colony-forming cell (CFC) progenitors in 2 mL SF methylcellulose-based medium (StemCell Technologies) containing SCF (50 ng/mL), EPO (3 U/mL), GM-CSF (50 ng/mL), G-CSF (50 ng/mL), IL-3 (20 ng/mL), and IL-6 (20 ng/mL), which was supplemented with 0.5% EX-CYTE (Millipore Bioscience Research Reagents, Temecula, CA).

    Techniques:

    Genomic rearrangement at 13q34. The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.

    Journal: BMC Medical Genetics

    Article Title: Dystonia, facial dysmorphism, intellectual disability and breast cancer associated with a chromosome 13q34 duplication and overexpression of TFDP1: case report

    doi: 10.1186/1471-2350-14-70

    Figure Lengend Snippet: Genomic rearrangement at 13q34. The 218,345 bp duplication is shown beneath gene tracks adapted from the UCSC Genome Browser (GRCH37/hg19 Assembly). The nucleotide sequence for the 69 bp fragment, possibly duplicated from an LTR located in Intron 3 of TFDP1 , is shown in upper case red lettering.

    Article Snippet: Identification of exact breakpoints was facilitated by mapping flanking SNPs and Affymetrix copy number (CN) probes for the 13q34 duplication in both the proband and her father (bolded were predicted by Quest Diagnostics to be within the gain): SNP_A-1803536 (Chr13:114022946), CN_634194 (Chr13:114023445), SNP_A-8304155 (Chr13:114023625), CN_091810(Chr13:114025424) , CN_634195(Chr13:114027458) , SNP_A-2261043(Chr13:114030927) , SNP_A-8505553(Chr13:114249807), CN_091834(Chr13:114249942) , CN_636300 (Chr13:114257699), and SNP_A-2105146(Chr13:114257910).

    Techniques: Sequencing