Structured Review

Illumina Inc microarray oligonucleotides
Schematic of in situ replication of DNA molecules from next-generation sequencing (NGS) platforms and subsequent PCR-based retrieval of target sequences. ( A ) Process flow chart for PCR-based methods for the retrieval of error-free DNA targets from an NGS-replica pool. ( B ) Preparation strategy of 454 GS Junior sequencing-based retrieval. Combinatorial barcode-tagged (CBT) pools were processed from <t>microarray-synthesized</t> oligonucleotides and subsequently ligated to the sheared genomic DNA as flanking sequences. The library was replicated in a sealed NGS plate. ( C ) Preparation strategy of a pre-NGS pool (MiSeq and Ion Proton). The barcoded library (cgc50 pool) was directly synthesized on a microarray. ( D ) Schematic of library replication in a MiSeq flow cell. ( E ) Schematic of library replication using melt-off DNA in the Ion Proton system. This process could be automatically performed using an Ion OneTouch™ ES system.
Microarray Oligonucleotides, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 98/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/microarray oligonucleotides/product/Illumina Inc
Average 98 stars, based on 3 article reviews
Price from $9.99 to $1999.99
microarray oligonucleotides - by Bioz Stars, 2020-03
98/100 stars

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1) Product Images from "Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms"

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms

Journal: Nucleic Acids Research

doi: 10.1093/nar/gky016

Schematic of in situ replication of DNA molecules from next-generation sequencing (NGS) platforms and subsequent PCR-based retrieval of target sequences. ( A ) Process flow chart for PCR-based methods for the retrieval of error-free DNA targets from an NGS-replica pool. ( B ) Preparation strategy of 454 GS Junior sequencing-based retrieval. Combinatorial barcode-tagged (CBT) pools were processed from microarray-synthesized oligonucleotides and subsequently ligated to the sheared genomic DNA as flanking sequences. The library was replicated in a sealed NGS plate. ( C ) Preparation strategy of a pre-NGS pool (MiSeq and Ion Proton). The barcoded library (cgc50 pool) was directly synthesized on a microarray. ( D ) Schematic of library replication in a MiSeq flow cell. ( E ) Schematic of library replication using melt-off DNA in the Ion Proton system. This process could be automatically performed using an Ion OneTouch™ ES system.
Figure Legend Snippet: Schematic of in situ replication of DNA molecules from next-generation sequencing (NGS) platforms and subsequent PCR-based retrieval of target sequences. ( A ) Process flow chart for PCR-based methods for the retrieval of error-free DNA targets from an NGS-replica pool. ( B ) Preparation strategy of 454 GS Junior sequencing-based retrieval. Combinatorial barcode-tagged (CBT) pools were processed from microarray-synthesized oligonucleotides and subsequently ligated to the sheared genomic DNA as flanking sequences. The library was replicated in a sealed NGS plate. ( C ) Preparation strategy of a pre-NGS pool (MiSeq and Ion Proton). The barcoded library (cgc50 pool) was directly synthesized on a microarray. ( D ) Schematic of library replication in a MiSeq flow cell. ( E ) Schematic of library replication using melt-off DNA in the Ion Proton system. This process could be automatically performed using an Ion OneTouch™ ES system.

Techniques Used: In Situ, Next-Generation Sequencing, Polymerase Chain Reaction, Flow Cytometry, Sequencing, Microarray, Synthesized

2) Product Images from "Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms"

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms

Journal: Nucleic Acids Research

doi: 10.1093/nar/gky016

Schematic of in situ replication of DNA molecules from next-generation sequencing (NGS) platforms and subsequent PCR-based retrieval of target sequences. ( A ) Process flow chart for PCR-based methods for the retrieval of error-free DNA targets from an NGS-replica pool. ( B ) Preparation strategy of 454 GS Junior sequencing-based retrieval. Combinatorial barcode-tagged (CBT) pools were processed from microarray-synthesized oligonucleotides and subsequently ligated to the sheared genomic DNA as flanking sequences. The library was replicated in a sealed NGS plate. ( C ) Preparation strategy of a pre-NGS pool (MiSeq and Ion Proton). The barcoded library (cgc50 pool) was directly synthesized on a microarray. ( D ) Schematic of library replication in a MiSeq flow cell. ( E ) Schematic of library replication using melt-off DNA in the Ion Proton system. This process could be automatically performed using an Ion OneTouch™ ES system.
Figure Legend Snippet: Schematic of in situ replication of DNA molecules from next-generation sequencing (NGS) platforms and subsequent PCR-based retrieval of target sequences. ( A ) Process flow chart for PCR-based methods for the retrieval of error-free DNA targets from an NGS-replica pool. ( B ) Preparation strategy of 454 GS Junior sequencing-based retrieval. Combinatorial barcode-tagged (CBT) pools were processed from microarray-synthesized oligonucleotides and subsequently ligated to the sheared genomic DNA as flanking sequences. The library was replicated in a sealed NGS plate. ( C ) Preparation strategy of a pre-NGS pool (MiSeq and Ion Proton). The barcoded library (cgc50 pool) was directly synthesized on a microarray. ( D ) Schematic of library replication in a MiSeq flow cell. ( E ) Schematic of library replication using melt-off DNA in the Ion Proton system. This process could be automatically performed using an Ion OneTouch™ ES system.

Techniques Used: In Situ, Next-Generation Sequencing, Polymerase Chain Reaction, Flow Cytometry, Sequencing, Microarray, Synthesized

Related Articles

Flow Cytometry:

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: CBT-labeled DNA library preparation for Illumina sequencing-based experiment To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. With Illumina MiSeq instrument, the product was sequenced and analyzed, and NGS-replica pool was obtained from flow-cell.

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. With Illumina MiSeq instrument, the product was sequenced and analyzed, and NGS-replica pool was obtained from flow-cell.

Synthesized:

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: .. CBT-labeled DNA library preparation for Illumina sequencing-based experiment To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. Then, cgc50 pool was labeled with CBT library using the same protocol of 454-based experiment with primers listed in .

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: .. To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. Then, cgc50 pool was labeled with CBT library using the same protocol of 454-based experiment with primers listed in .

Next-Generation Sequencing:

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: CBT-labeled DNA library preparation for Illumina sequencing-based experiment To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. With Illumina MiSeq instrument, the product was sequenced and analyzed, and NGS-replica pool was obtained from flow-cell.

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. With Illumina MiSeq instrument, the product was sequenced and analyzed, and NGS-replica pool was obtained from flow-cell.

Labeling:

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: .. CBT-labeled DNA library preparation for Illumina sequencing-based experiment To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. Then, cgc50 pool was labeled with CBT library using the same protocol of 454-based experiment with primers listed in .

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: .. To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. Then, cgc50 pool was labeled with CBT library using the same protocol of 454-based experiment with primers listed in .

Microarray:

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: .. CBT-labeled DNA library preparation for Illumina sequencing-based experiment To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. Then, cgc50 pool was labeled with CBT library using the same protocol of 454-based experiment with primers listed in .

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: .. To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. Then, cgc50 pool was labeled with CBT library using the same protocol of 454-based experiment with primers listed in .

Sequencing:

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: .. CBT-labeled DNA library preparation for Illumina sequencing-based experiment To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ). .. Then, cgc50 pool was labeled with CBT library using the same protocol of 454-based experiment with primers listed in .

Article Title: Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms
Article Snippet: Paragraph title: CBT-labeled DNA library preparation for Illumina sequencing-based experiment ... To use the CBT-based labeling method on the Illumina sequencer, another microarray oligonucleotides, consisting of cgc50 pool and CBT library, were redesigned and synthesized to be compatible with the Illumina platform ( ).

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    Illumina Inc illumina dna microarray
    Fold change (FC) values of upregulated ( red ) and downregulated ( green ) genes in dexmedetomidine-treated (100 nM) A7r5-α 2B vascular smooth muscle cells compared with vehicle-treated control cells in the <t>Illumina</t> <t>DNA</t> <t>microarray.</t> The genes are ordered based on the associated adjusted p- values, in decreasing order. Explanation of gene symbols, actual and adjusted p- values can be found in Additional file 2
    Illumina Dna Microarray, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    81
    Illumina Inc mouse ref v2 0 gene chip array
    Cosmc controls diverse host pathways that regulate the microbiota and inflammation in the distal colon. Epithelial cells were purified from the CR or SI from KO and WT mice, and gene expression was performed on Illumina mouse ref 8 <t>v2.0</t> expression chip.
    Mouse Ref V2 0 Gene Chip Array, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 81/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    83
    Illumina Inc anti hb9 po4 chip dna
    Identification of Nono as a phospho-HLXB9 interacting protein. A , overexpression of HLXB9 shows both its phosphorylated and unphosphorylated isoform. WCE were prepared from MIN6-4N cells transfected with myc-His-tag empty vector ( mh-Vector ) or plasmids expressing myc-his-tagged HLXB9 ( <t>mh-HB9-WT</t> ) or the phospho-dead mutant of HLXB9 with alanine substitution at Ser-78 and Ser-80 ( mh-HB9-AA ). WCE were run on the same gel to generate two Western blots to probe with anti-myc-tag or <t>anti-HB9-PO4</t> (phospho-HLXB9 antibody). To analyze the bands, the blots were placed side-by-side (indicated by the dotted line ). The top band of the doublet in the lane marked mh-HB9-WT corresponds to phospho-HLXB9 because it is not detected with the myc-tag antibody in mh-HB9-AA, and it is detected specifically with anti-HB9-PO4. The bottom band of the doublet corresponds to the unphosphorylated isoform of HLXB9 ( HB9-unPO4 ) because it is not detected with anti-HB9-PO4. β-Actin was used as the loading control. B , large scale co-IP shows the two isoforms of HLXB9 and co-immunoprecipitating proteins. Silver-stained gel of proteins separated on SDS-PAGE after large scale co-IP with a myc-tag antibody using WCE prepared in A . As also seen by Western blot analysis in A , the bands marked SDMS1 and SDMS3 show the doublet in mh-HB9-WT Co-IP (PO4-HB9 and unPO4-HB9) and a single band in mh-HB9-AA corresponding to unPO4-HB9. Bands marked SDMS1 , SDMS2 , SDMS3 , and SDMS4 (that were absent in the mh-Vector lane) were excised from the gel and subjected to mass spectrometry analysis. C , Nono uniquely co-immunoprecipitates with phospho-HLXB9. The number of peptides (total and unique) in the bands excised from the gel shown in B and their corresponding proteins is shown. Several proteins were present in both the mh-HB9-WT and mh-HB9-AA immunoprecipitates. The protein Nono emerged as a phospho-HLXB9-specific partner found only in the co-IP of mh-HB9-WT and not in the co-IP of the phospho-dead mutant of HLXB9 (mh-HB9-AA). D , overexpressed HLXB9 can Co-IP with endogenous Nono. Western blot ( WB ) probed with anti-myc-tag showing specific co-IP of HLXB9 with Nono using WCE of MIN6-4N cells transfected with mh-HB9-WT. Anti-HA-tag was used as a negative control. Higher exposure ( top panel ) and lower exposure ( bottom panel ) of the blot are shown to clearly visualize the input HLXB9 bands. IP , immunoprecipitation. E , endogenous phospho-HLXB9 can co-immunoprecipitate with endogenous Nono. Western blots probed with anti-Nono and anti-HB9 show specific co-IP of endogenous Nono with endogenous phospho-HLXB9 using WCE of MIN6-4N cells. An anti-HA-tag was used as a negative control.
    Anti Hb9 Po4 Chip Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 83/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Illumina Inc ubtf1 2 chip dna
    <t>Ubtf1/2</t> knockdown leads to <t>DNA</t> damage and genomic instability. ( A ) NIH3T3 cells were transfected with sir Egfp or sir Ubtf1/2 #1 for 48 h and DNA damage was measured by comet assay. Representative images of SYBR green-stained DNA of sir Egfp control cells,
    Ubtf1 2 Chip Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Fold change (FC) values of upregulated ( red ) and downregulated ( green ) genes in dexmedetomidine-treated (100 nM) A7r5-α 2B vascular smooth muscle cells compared with vehicle-treated control cells in the Illumina DNA microarray. The genes are ordered based on the associated adjusted p- values, in decreasing order. Explanation of gene symbols, actual and adjusted p- values can be found in Additional file 2

    Journal: BMC Systems Biology

    Article Title: Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells

    doi: 10.1186/s12918-017-0439-8

    Figure Lengend Snippet: Fold change (FC) values of upregulated ( red ) and downregulated ( green ) genes in dexmedetomidine-treated (100 nM) A7r5-α 2B vascular smooth muscle cells compared with vehicle-treated control cells in the Illumina DNA microarray. The genes are ordered based on the associated adjusted p- values, in decreasing order. Explanation of gene symbols, actual and adjusted p- values can be found in Additional file 2

    Article Snippet: Illumina DNA microarray The objective of this set of experiments was to identify specific genes involved in α2B -adrenoceptor-evoked VSMC proliferation.

    Techniques: Microarray

    Cosmc controls diverse host pathways that regulate the microbiota and inflammation in the distal colon. Epithelial cells were purified from the CR or SI from KO and WT mice, and gene expression was performed on Illumina mouse ref 8 v2.0 expression chip.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Cosmc is an X-linked inflammatory bowel disease risk gene that spatially regulates gut microbiota and contributes to sex-specific risk

    doi: 10.1073/pnas.1612158114

    Figure Lengend Snippet: Cosmc controls diverse host pathways that regulate the microbiota and inflammation in the distal colon. Epithelial cells were purified from the CR or SI from KO and WT mice, and gene expression was performed on Illumina mouse ref 8 v2.0 expression chip.

    Article Snippet: To identify host pathways that may contribute to regional changes in the microbiota, we isolated colorectal (CR) and small intestine (SI) epithelia from ∼2-mo-old male WT and KO mice, before clinical inflammation and at the same age as 16S sequencing, and analyzed transcripts with Illumina Mouse-Ref v2.0 gene chip array ( n = 4 mice/group per region) ( ).

    Techniques: Purification, Mouse Assay, Expressing, Chromatin Immunoprecipitation

    Identification of Nono as a phospho-HLXB9 interacting protein. A , overexpression of HLXB9 shows both its phosphorylated and unphosphorylated isoform. WCE were prepared from MIN6-4N cells transfected with myc-His-tag empty vector ( mh-Vector ) or plasmids expressing myc-his-tagged HLXB9 ( mh-HB9-WT ) or the phospho-dead mutant of HLXB9 with alanine substitution at Ser-78 and Ser-80 ( mh-HB9-AA ). WCE were run on the same gel to generate two Western blots to probe with anti-myc-tag or anti-HB9-PO4 (phospho-HLXB9 antibody). To analyze the bands, the blots were placed side-by-side (indicated by the dotted line ). The top band of the doublet in the lane marked mh-HB9-WT corresponds to phospho-HLXB9 because it is not detected with the myc-tag antibody in mh-HB9-AA, and it is detected specifically with anti-HB9-PO4. The bottom band of the doublet corresponds to the unphosphorylated isoform of HLXB9 ( HB9-unPO4 ) because it is not detected with anti-HB9-PO4. β-Actin was used as the loading control. B , large scale co-IP shows the two isoforms of HLXB9 and co-immunoprecipitating proteins. Silver-stained gel of proteins separated on SDS-PAGE after large scale co-IP with a myc-tag antibody using WCE prepared in A . As also seen by Western blot analysis in A , the bands marked SDMS1 and SDMS3 show the doublet in mh-HB9-WT Co-IP (PO4-HB9 and unPO4-HB9) and a single band in mh-HB9-AA corresponding to unPO4-HB9. Bands marked SDMS1 , SDMS2 , SDMS3 , and SDMS4 (that were absent in the mh-Vector lane) were excised from the gel and subjected to mass spectrometry analysis. C , Nono uniquely co-immunoprecipitates with phospho-HLXB9. The number of peptides (total and unique) in the bands excised from the gel shown in B and their corresponding proteins is shown. Several proteins were present in both the mh-HB9-WT and mh-HB9-AA immunoprecipitates. The protein Nono emerged as a phospho-HLXB9-specific partner found only in the co-IP of mh-HB9-WT and not in the co-IP of the phospho-dead mutant of HLXB9 (mh-HB9-AA). D , overexpressed HLXB9 can Co-IP with endogenous Nono. Western blot ( WB ) probed with anti-myc-tag showing specific co-IP of HLXB9 with Nono using WCE of MIN6-4N cells transfected with mh-HB9-WT. Anti-HA-tag was used as a negative control. Higher exposure ( top panel ) and lower exposure ( bottom panel ) of the blot are shown to clearly visualize the input HLXB9 bands. IP , immunoprecipitation. E , endogenous phospho-HLXB9 can co-immunoprecipitate with endogenous Nono. Western blots probed with anti-Nono and anti-HB9 show specific co-IP of endogenous Nono with endogenous phospho-HLXB9 using WCE of MIN6-4N cells. An anti-HA-tag was used as a negative control.

    Journal: The Journal of Biological Chemistry

    Article Title: Pro-oncogenic Roles of HLXB9 Protein in Insulinoma Cells through Interaction with Nono Protein and Down-regulation of the c-Met Inhibitor Cblb (Casitas B-lineage Lymphoma b) *

    doi: 10.1074/jbc.M115.661413

    Figure Lengend Snippet: Identification of Nono as a phospho-HLXB9 interacting protein. A , overexpression of HLXB9 shows both its phosphorylated and unphosphorylated isoform. WCE were prepared from MIN6-4N cells transfected with myc-His-tag empty vector ( mh-Vector ) or plasmids expressing myc-his-tagged HLXB9 ( mh-HB9-WT ) or the phospho-dead mutant of HLXB9 with alanine substitution at Ser-78 and Ser-80 ( mh-HB9-AA ). WCE were run on the same gel to generate two Western blots to probe with anti-myc-tag or anti-HB9-PO4 (phospho-HLXB9 antibody). To analyze the bands, the blots were placed side-by-side (indicated by the dotted line ). The top band of the doublet in the lane marked mh-HB9-WT corresponds to phospho-HLXB9 because it is not detected with the myc-tag antibody in mh-HB9-AA, and it is detected specifically with anti-HB9-PO4. The bottom band of the doublet corresponds to the unphosphorylated isoform of HLXB9 ( HB9-unPO4 ) because it is not detected with anti-HB9-PO4. β-Actin was used as the loading control. B , large scale co-IP shows the two isoforms of HLXB9 and co-immunoprecipitating proteins. Silver-stained gel of proteins separated on SDS-PAGE after large scale co-IP with a myc-tag antibody using WCE prepared in A . As also seen by Western blot analysis in A , the bands marked SDMS1 and SDMS3 show the doublet in mh-HB9-WT Co-IP (PO4-HB9 and unPO4-HB9) and a single band in mh-HB9-AA corresponding to unPO4-HB9. Bands marked SDMS1 , SDMS2 , SDMS3 , and SDMS4 (that were absent in the mh-Vector lane) were excised from the gel and subjected to mass spectrometry analysis. C , Nono uniquely co-immunoprecipitates with phospho-HLXB9. The number of peptides (total and unique) in the bands excised from the gel shown in B and their corresponding proteins is shown. Several proteins were present in both the mh-HB9-WT and mh-HB9-AA immunoprecipitates. The protein Nono emerged as a phospho-HLXB9-specific partner found only in the co-IP of mh-HB9-WT and not in the co-IP of the phospho-dead mutant of HLXB9 (mh-HB9-AA). D , overexpressed HLXB9 can Co-IP with endogenous Nono. Western blot ( WB ) probed with anti-myc-tag showing specific co-IP of HLXB9 with Nono using WCE of MIN6-4N cells transfected with mh-HB9-WT. Anti-HA-tag was used as a negative control. Higher exposure ( top panel ) and lower exposure ( bottom panel ) of the blot are shown to clearly visualize the input HLXB9 bands. IP , immunoprecipitation. E , endogenous phospho-HLXB9 can co-immunoprecipitate with endogenous Nono. Western blots probed with anti-Nono and anti-HB9 show specific co-IP of endogenous Nono with endogenous phospho-HLXB9 using WCE of MIN6-4N cells. An anti-HA-tag was used as a negative control.

    Article Snippet: Purified input DNA and anti-HB9-PO4-ChIP DNA were used to prepare ChIP-Seq libraries (Illumina), and the two libraries were sequenced for 51 bp (Illumina, NIDDK Genomics Core).

    Techniques: Over Expression, Transfection, Plasmid Preparation, Expressing, Mutagenesis, Western Blot, Co-Immunoprecipitation Assay, Staining, SDS Page, Mass Spectrometry, Negative Control, Immunoprecipitation

    HLXB9 suppresses the expression of Cblb mRNA by suppressing Cblb promoter activity. A and B , among targets identified by anti-HB9-PO4 ChIP-Seq, the expression of only Arid1b and Cblb was affected by HLXB9. Quantitative RT-PCR is shown of the indicated genes using RNA prepared from MIN6-4N cells transfected with control siRNA ( siC ) or HLXB9 siRNA ( siHB9 ), empty vector, or mh-HB9-WT. A , Western blot confirming knockdown or overexpression of HLXB9 with anti-HLXB9 or anti-myc-tag, respectively, and β-actin as the loading control. B , HLXB9 knockdown or overexpression regulated the relative mRNA level of only two genes (Arid1b and Cblb). Both were reduced upon HLXB9 overexpression, but only Cblb was increased upon HLXB9 knockdown. Error bar = mean and S.D. from three experiments. * = p

    Journal: The Journal of Biological Chemistry

    Article Title: Pro-oncogenic Roles of HLXB9 Protein in Insulinoma Cells through Interaction with Nono Protein and Down-regulation of the c-Met Inhibitor Cblb (Casitas B-lineage Lymphoma b) *

    doi: 10.1074/jbc.M115.661413

    Figure Lengend Snippet: HLXB9 suppresses the expression of Cblb mRNA by suppressing Cblb promoter activity. A and B , among targets identified by anti-HB9-PO4 ChIP-Seq, the expression of only Arid1b and Cblb was affected by HLXB9. Quantitative RT-PCR is shown of the indicated genes using RNA prepared from MIN6-4N cells transfected with control siRNA ( siC ) or HLXB9 siRNA ( siHB9 ), empty vector, or mh-HB9-WT. A , Western blot confirming knockdown or overexpression of HLXB9 with anti-HLXB9 or anti-myc-tag, respectively, and β-actin as the loading control. B , HLXB9 knockdown or overexpression regulated the relative mRNA level of only two genes (Arid1b and Cblb). Both were reduced upon HLXB9 overexpression, but only Cblb was increased upon HLXB9 knockdown. Error bar = mean and S.D. from three experiments. * = p

    Article Snippet: Purified input DNA and anti-HB9-PO4-ChIP DNA were used to prepare ChIP-Seq libraries (Illumina), and the two libraries were sequenced for 51 bp (Illumina, NIDDK Genomics Core).

    Techniques: Expressing, Activity Assay, Chromatin Immunoprecipitation, Quantitative RT-PCR, Transfection, Plasmid Preparation, Western Blot, Over Expression

    HLXB9 binding motif in the Cblb promoter. A , consensus motif in anti-HB9-PO4 ChIP-Seq tags located at promoter regions. De novo ). B , sequence of the HLXB9 binding motifs in the Cblb promoter. The top line shows the putative HLXB9 binding motifs ( red ) in the DNA sequence of the Cblb promoter (−741 to −710 region from the transcriptional start site is shown). The bottom line shows nucleotide substitutions ( blue ) to mutate the motifs by site-directed mutagenesis in the Cblb-promoter construct used in C. C and D , HLXB9 did not suppress the activity of the Cblb promoter containing mutations at the HLXB9 binding motifs. The putative HLXB9 binding motifs shown in B were mutated by site-directed mutagenesis of the PG02-Cblb promoter construct and analyzed for promoter activity in MIN6-4N cells. RLU for each of the transfections are shown. Compared with the empty vector PG02, the PG02-Cblb-SDM2 plasmid showed significantly high RLU and co-expression of increasing amounts of HLXB9 did not suppress the Cblb promoter activity. Error bar = Mean and S.D. from 3 experiments, * = p

    Journal: The Journal of Biological Chemistry

    Article Title: Pro-oncogenic Roles of HLXB9 Protein in Insulinoma Cells through Interaction with Nono Protein and Down-regulation of the c-Met Inhibitor Cblb (Casitas B-lineage Lymphoma b) *

    doi: 10.1074/jbc.M115.661413

    Figure Lengend Snippet: HLXB9 binding motif in the Cblb promoter. A , consensus motif in anti-HB9-PO4 ChIP-Seq tags located at promoter regions. De novo ). B , sequence of the HLXB9 binding motifs in the Cblb promoter. The top line shows the putative HLXB9 binding motifs ( red ) in the DNA sequence of the Cblb promoter (−741 to −710 region from the transcriptional start site is shown). The bottom line shows nucleotide substitutions ( blue ) to mutate the motifs by site-directed mutagenesis in the Cblb-promoter construct used in C. C and D , HLXB9 did not suppress the activity of the Cblb promoter containing mutations at the HLXB9 binding motifs. The putative HLXB9 binding motifs shown in B were mutated by site-directed mutagenesis of the PG02-Cblb promoter construct and analyzed for promoter activity in MIN6-4N cells. RLU for each of the transfections are shown. Compared with the empty vector PG02, the PG02-Cblb-SDM2 plasmid showed significantly high RLU and co-expression of increasing amounts of HLXB9 did not suppress the Cblb promoter activity. Error bar = Mean and S.D. from 3 experiments, * = p

    Article Snippet: Purified input DNA and anti-HB9-PO4-ChIP DNA were used to prepare ChIP-Seq libraries (Illumina), and the two libraries were sequenced for 51 bp (Illumina, NIDDK Genomics Core).

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Sequencing, Mutagenesis, Construct, Activity Assay, Transfection, Plasmid Preparation, Expressing

    HLXB9 co-localizes with Nono in the nucleus, and co-overexpression of HLXB9 and Nono decreases the overexpression of Nono with translocation of HLXB9 into the cytoplasm. A , endogenous phospho-HLXB9 co-localizes with endogenous Nono in the nucleus. IF images of MIN6-4N cells show endogenous Nono ( red ) and phospho-HLXB9 ( green ). DAPI was used to detect the nuclei ( blue ). A merged image of the red and green IF shows co-localization of Nono and phospho-HLXB9 in subnuclear spots and some regions with phospho-HLXB9 ( green ) that did not co-localize with Nono. B , overexpression of HLXB9 decreases the level of overexpressed Nono protein. Western blots are shown of WCE and the pellet leftover after WCE preparation from MIN6-4N cells expressing mh-HB9-WT, FLAG-Nono, or both together. Empty vector DNA ( Vec ) was used to maintain the same amount of DNA in the transfections. The expression of transfected HLXB9 was detected with the anti-myc-tag; Nono was detected with the anti-FLAG-tag and with anti-Nono to detect both endogenous and transfected FLAG-tagged Nono. β-Actin was used as the loading control. Endogenous Nono levels were not affected by HLXB9 overexpression. However, the level of transfected FLAG-Nono was reduced upon HLXB9 overexpression. A similar pattern of bands was seen in the pellet leftover after WCE preparation, indicating that the reduced level of Nono upon HLXB9 overexpression was not due to differential cell lysis in the WCE preparation. C , HLXB9 did not reduce the expression of endogenous Nono protein. Western blot analysis to detect endogenous HLXB9 and Nono using WCE prepared from MIN6-4N cells transfected with control siRNA ( siC ) or HLXB9 siRNA ( siHB9 ) is shown. p84 was used as the loading control. HLXB9 was significantly knocked down, but that did not affect the level of endogenous Nono. D , co-overexpression of HLXB9 and Nono reduces the level of Nono protein in the nucleus with translocation of HLXB9 to the cytoplasm. Shown is Western blot analysis of subcellular fractionation of CE, NE, and CB/PE from MIN6-4N cells expressing mh-HB9-WT, FLAG-Nono, or both together. Empty vector DNA ( Vec ) was used to maintain the same amount of DNA in the transfections. The expression of transfected HLXB9 was detected with the anti-myc-tag; Nono was detected with the anti-FLAG-tag; detection of marker proteins (Hsp90 for CE, p84 for NE, and histone H3 for CB/PE) showed minimal cross-contamination of the fractions and also served as loading controls for each fraction. Overexpressed Nono was found in the NE and in the CB/PE, but its level in NE was reduced by HLXB9 overexpression. Overexpressed HLXB9 was mostly located in the CB/PE and with a significant amount in the nucleus, but it was also detected in the CE by Nono overexpression.

    Journal: The Journal of Biological Chemistry

    Article Title: Pro-oncogenic Roles of HLXB9 Protein in Insulinoma Cells through Interaction with Nono Protein and Down-regulation of the c-Met Inhibitor Cblb (Casitas B-lineage Lymphoma b) *

    doi: 10.1074/jbc.M115.661413

    Figure Lengend Snippet: HLXB9 co-localizes with Nono in the nucleus, and co-overexpression of HLXB9 and Nono decreases the overexpression of Nono with translocation of HLXB9 into the cytoplasm. A , endogenous phospho-HLXB9 co-localizes with endogenous Nono in the nucleus. IF images of MIN6-4N cells show endogenous Nono ( red ) and phospho-HLXB9 ( green ). DAPI was used to detect the nuclei ( blue ). A merged image of the red and green IF shows co-localization of Nono and phospho-HLXB9 in subnuclear spots and some regions with phospho-HLXB9 ( green ) that did not co-localize with Nono. B , overexpression of HLXB9 decreases the level of overexpressed Nono protein. Western blots are shown of WCE and the pellet leftover after WCE preparation from MIN6-4N cells expressing mh-HB9-WT, FLAG-Nono, or both together. Empty vector DNA ( Vec ) was used to maintain the same amount of DNA in the transfections. The expression of transfected HLXB9 was detected with the anti-myc-tag; Nono was detected with the anti-FLAG-tag and with anti-Nono to detect both endogenous and transfected FLAG-tagged Nono. β-Actin was used as the loading control. Endogenous Nono levels were not affected by HLXB9 overexpression. However, the level of transfected FLAG-Nono was reduced upon HLXB9 overexpression. A similar pattern of bands was seen in the pellet leftover after WCE preparation, indicating that the reduced level of Nono upon HLXB9 overexpression was not due to differential cell lysis in the WCE preparation. C , HLXB9 did not reduce the expression of endogenous Nono protein. Western blot analysis to detect endogenous HLXB9 and Nono using WCE prepared from MIN6-4N cells transfected with control siRNA ( siC ) or HLXB9 siRNA ( siHB9 ) is shown. p84 was used as the loading control. HLXB9 was significantly knocked down, but that did not affect the level of endogenous Nono. D , co-overexpression of HLXB9 and Nono reduces the level of Nono protein in the nucleus with translocation of HLXB9 to the cytoplasm. Shown is Western blot analysis of subcellular fractionation of CE, NE, and CB/PE from MIN6-4N cells expressing mh-HB9-WT, FLAG-Nono, or both together. Empty vector DNA ( Vec ) was used to maintain the same amount of DNA in the transfections. The expression of transfected HLXB9 was detected with the anti-myc-tag; Nono was detected with the anti-FLAG-tag; detection of marker proteins (Hsp90 for CE, p84 for NE, and histone H3 for CB/PE) showed minimal cross-contamination of the fractions and also served as loading controls for each fraction. Overexpressed Nono was found in the NE and in the CB/PE, but its level in NE was reduced by HLXB9 overexpression. Overexpressed HLXB9 was mostly located in the CB/PE and with a significant amount in the nucleus, but it was also detected in the CE by Nono overexpression.

    Article Snippet: Purified input DNA and anti-HB9-PO4-ChIP DNA were used to prepare ChIP-Seq libraries (Illumina), and the two libraries were sequenced for 51 bp (Illumina, NIDDK Genomics Core).

    Techniques: Over Expression, Translocation Assay, Western Blot, Expressing, Plasmid Preparation, Transfection, FLAG-tag, Lysis, Fractionation, Marker

    Increased phospho-HLXB9, decreased Cblb, and increased c-Met in insulinoma from the conventional mouse model of menin loss ( Men1 +/− ). Shown are images of immunofluorescence for insulin and IHC for the indicated proteins in the pancreas section of an 18-month-old Men1 +/− mouse. Insulin staining shows the location of the normal-looking islet ( panels on the left ) and the large islet tumor that covers the entire viewing field ( panels on the right ). Compared with a normal-looking insulin-positive islet in the same section, the insulin-positive islet tumor shows increased nuclear staining for HB9 and HB9-PO4 and increased nuclear and cytoplasmic staining for c-Met but almost no staining for Cblb (cytoplasm).

    Journal: The Journal of Biological Chemistry

    Article Title: Pro-oncogenic Roles of HLXB9 Protein in Insulinoma Cells through Interaction with Nono Protein and Down-regulation of the c-Met Inhibitor Cblb (Casitas B-lineage Lymphoma b) *

    doi: 10.1074/jbc.M115.661413

    Figure Lengend Snippet: Increased phospho-HLXB9, decreased Cblb, and increased c-Met in insulinoma from the conventional mouse model of menin loss ( Men1 +/− ). Shown are images of immunofluorescence for insulin and IHC for the indicated proteins in the pancreas section of an 18-month-old Men1 +/− mouse. Insulin staining shows the location of the normal-looking islet ( panels on the left ) and the large islet tumor that covers the entire viewing field ( panels on the right ). Compared with a normal-looking insulin-positive islet in the same section, the insulin-positive islet tumor shows increased nuclear staining for HB9 and HB9-PO4 and increased nuclear and cytoplasmic staining for c-Met but almost no staining for Cblb (cytoplasm).

    Article Snippet: Purified input DNA and anti-HB9-PO4-ChIP DNA were used to prepare ChIP-Seq libraries (Illumina), and the two libraries were sequenced for 51 bp (Illumina, NIDDK Genomics Core).

    Techniques: Immunofluorescence, Immunohistochemistry, Staining

    Increased phospho-HLXB9, decreased Cblb, and increased c-Met in insulinoma from the conditional mouse model of menin loss (RIP-Cre- Men1 f/f ). Images of immunofluorescence for insulin and IHC for the indicated proteins in pancreas sections from a 12-month-old Men1 f/f mouse and RIP-Cre- Men1 f/f mouse. Compared with the insulin-positive normal islet ( panels on the left ), the large insulin-positive islet tumor that covers the entire viewing field ( panels on the right ) shows increased nuclear staining for HB9 and HB9-PO4, increased nuclear and cytoplasmic staining for c-Met, and decreased staining for Cblb (cytoplasm).

    Journal: The Journal of Biological Chemistry

    Article Title: Pro-oncogenic Roles of HLXB9 Protein in Insulinoma Cells through Interaction with Nono Protein and Down-regulation of the c-Met Inhibitor Cblb (Casitas B-lineage Lymphoma b) *

    doi: 10.1074/jbc.M115.661413

    Figure Lengend Snippet: Increased phospho-HLXB9, decreased Cblb, and increased c-Met in insulinoma from the conditional mouse model of menin loss (RIP-Cre- Men1 f/f ). Images of immunofluorescence for insulin and IHC for the indicated proteins in pancreas sections from a 12-month-old Men1 f/f mouse and RIP-Cre- Men1 f/f mouse. Compared with the insulin-positive normal islet ( panels on the left ), the large insulin-positive islet tumor that covers the entire viewing field ( panels on the right ) shows increased nuclear staining for HB9 and HB9-PO4, increased nuclear and cytoplasmic staining for c-Met, and decreased staining for Cblb (cytoplasm).

    Article Snippet: Purified input DNA and anti-HB9-PO4-ChIP DNA were used to prepare ChIP-Seq libraries (Illumina), and the two libraries were sequenced for 51 bp (Illumina, NIDDK Genomics Core).

    Techniques: Immunofluorescence, Immunohistochemistry, Staining

    Identification of Cblb as a phospho-HLXB9 target gene. A , the anti-HB9-PO4 antibody specifically recognizes the phosphorylated isoform of HLXB9. WCE and chromatin were prepared from MIN6-4N cells transfected with a plasmid expressing myc-his-tagged HLXB9 ( mh-HB9-WT ). WCE was used IP with rabbit antibodies anti-myc-tag or anti-HB9-PO4 and detected by Western blot ( WB ) with mouse anti-myc-tag. Rabbit anti-HA-tag was used as the negative control. The input WCE and anti-myc-tag IP display a doublet corresponding to phospho-HLXB9 and unphosphorylated HLXB9. Anti-HB9-PO4 could specifically immunoprecipitate phospho-HLXB9 corresponding to the top band of the doublet. B , significant enrichment of promoter regions among the anti-HB9-PO4 ChIP-Seq tags. Chromatin prepared from MIN6-4N cells transfected in A was used for ChIP with anti-HB9-PO4. DNA obtained before and after ChIP was used for preparing libraries followed by deep sequencing (ChIP-Seq) and mapping of the anti-HB9-PO4-specific ChIP-Seq tags to the mouse genome. The pie chart shows the percent distribution of tags in the mouse genome (a typical input library, Genomatix) and in the anti-HB9-PO4 ChIP-Seq at the indicated regions; 20% of the anti-HB9-PO4 ChIP-Seq tags were located near promoter regions and selected for further analysis. C , phospho-HLXB9 occupancy is highest at the Arid1b and Cblb gene in cells overexpressing HLXB9. ChIP-quantitative PCR assay for validating the 10 phospho-HLXB9 targets is shown as the percent of input chromatin DNA PCR for each primer pair. Chromatin prepared from MIN6-4N cells expressing mh-HB9-WT was used for anti-HB9-PO4 ChIP. Also shown is a Western blot confirming overexpression of HLXB9 (myc-tag antibody) and β-actin as the loading control. D , endogenous phospho-HLXB9 occupancy is highest at the Cblb gene. ChIP-quantitative PCR assay of the 10 phospho-HLXB9 targets is shown as percent of input chromatin DNA PCR for each primer pair. Chromatin prepared from MIN6-4N cells was used for endogenous anti-HB9-PO4 ChIP. Endogenous phospho-HLXB9 occupancy was only detected at Cblb. E and F , H3K4me3 at Cblb unaffected but reduced H3K27me3 upon HLXB9 knockdown. ChIP-quantitative PCR assay of the 10 phospho-HLXB9 targets is shown as the percent of input chromatin DNA PCR for each primer pair. Chromatin prepared from MIN6-4N cells transfected with control siRNA ( siC ) or HLXB9 siRNA ( siHB9 ) was used for endogenous anti-H3K4me3 ChIP ( E ) or H3K27me3 ChIP ( F ). Also shown is a Western blot confirming knockdown of HLXB9 (HLXB9 antibody) and β-actin as the loading control. In siC versus siHB9, reciprocal H3K4me3 or H3K27me3 at only Cblb was HLXB9 binding-dependent because endogenous phospho-HLXB9 was only found to occupy Cblb ( D ).

    Journal: The Journal of Biological Chemistry

    Article Title: Pro-oncogenic Roles of HLXB9 Protein in Insulinoma Cells through Interaction with Nono Protein and Down-regulation of the c-Met Inhibitor Cblb (Casitas B-lineage Lymphoma b) *

    doi: 10.1074/jbc.M115.661413

    Figure Lengend Snippet: Identification of Cblb as a phospho-HLXB9 target gene. A , the anti-HB9-PO4 antibody specifically recognizes the phosphorylated isoform of HLXB9. WCE and chromatin were prepared from MIN6-4N cells transfected with a plasmid expressing myc-his-tagged HLXB9 ( mh-HB9-WT ). WCE was used IP with rabbit antibodies anti-myc-tag or anti-HB9-PO4 and detected by Western blot ( WB ) with mouse anti-myc-tag. Rabbit anti-HA-tag was used as the negative control. The input WCE and anti-myc-tag IP display a doublet corresponding to phospho-HLXB9 and unphosphorylated HLXB9. Anti-HB9-PO4 could specifically immunoprecipitate phospho-HLXB9 corresponding to the top band of the doublet. B , significant enrichment of promoter regions among the anti-HB9-PO4 ChIP-Seq tags. Chromatin prepared from MIN6-4N cells transfected in A was used for ChIP with anti-HB9-PO4. DNA obtained before and after ChIP was used for preparing libraries followed by deep sequencing (ChIP-Seq) and mapping of the anti-HB9-PO4-specific ChIP-Seq tags to the mouse genome. The pie chart shows the percent distribution of tags in the mouse genome (a typical input library, Genomatix) and in the anti-HB9-PO4 ChIP-Seq at the indicated regions; 20% of the anti-HB9-PO4 ChIP-Seq tags were located near promoter regions and selected for further analysis. C , phospho-HLXB9 occupancy is highest at the Arid1b and Cblb gene in cells overexpressing HLXB9. ChIP-quantitative PCR assay for validating the 10 phospho-HLXB9 targets is shown as the percent of input chromatin DNA PCR for each primer pair. Chromatin prepared from MIN6-4N cells expressing mh-HB9-WT was used for anti-HB9-PO4 ChIP. Also shown is a Western blot confirming overexpression of HLXB9 (myc-tag antibody) and β-actin as the loading control. D , endogenous phospho-HLXB9 occupancy is highest at the Cblb gene. ChIP-quantitative PCR assay of the 10 phospho-HLXB9 targets is shown as percent of input chromatin DNA PCR for each primer pair. Chromatin prepared from MIN6-4N cells was used for endogenous anti-HB9-PO4 ChIP. Endogenous phospho-HLXB9 occupancy was only detected at Cblb. E and F , H3K4me3 at Cblb unaffected but reduced H3K27me3 upon HLXB9 knockdown. ChIP-quantitative PCR assay of the 10 phospho-HLXB9 targets is shown as the percent of input chromatin DNA PCR for each primer pair. Chromatin prepared from MIN6-4N cells transfected with control siRNA ( siC ) or HLXB9 siRNA ( siHB9 ) was used for endogenous anti-H3K4me3 ChIP ( E ) or H3K27me3 ChIP ( F ). Also shown is a Western blot confirming knockdown of HLXB9 (HLXB9 antibody) and β-actin as the loading control. In siC versus siHB9, reciprocal H3K4me3 or H3K27me3 at only Cblb was HLXB9 binding-dependent because endogenous phospho-HLXB9 was only found to occupy Cblb ( D ).

    Article Snippet: Purified input DNA and anti-HB9-PO4-ChIP DNA were used to prepare ChIP-Seq libraries (Illumina), and the two libraries were sequenced for 51 bp (Illumina, NIDDK Genomics Core).

    Techniques: Transfection, Plasmid Preparation, Expressing, Western Blot, Negative Control, Chromatin Immunoprecipitation, Sequencing, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Over Expression, Binding Assay

    Ubtf1/2 knockdown leads to DNA damage and genomic instability. ( A ) NIH3T3 cells were transfected with sir Egfp or sir Ubtf1/2 #1 for 48 h and DNA damage was measured by comet assay. Representative images of SYBR green-stained DNA of sir Egfp control cells,

    Journal: Genome Research

    Article Title: A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes

    doi: 10.1101/gr.176115.114

    Figure Lengend Snippet: Ubtf1/2 knockdown leads to DNA damage and genomic instability. ( A ) NIH3T3 cells were transfected with sir Egfp or sir Ubtf1/2 #1 for 48 h and DNA damage was measured by comet assay. Representative images of SYBR green-stained DNA of sir Egfp control cells,

    Article Snippet: For ChIP-seq of UBTF1/2 ChIP DNA and input gDNA from NIH3T3, libraries from two biological replicates were prepared for the Illumina Genome Analyzer II platform at Peter MacCallum Cancer Center.

    Techniques: Transfection, Single Cell Gel Electrophoresis, SYBR Green Assay, Staining