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Agilent technologies 2100 bioanalyzer instrument
Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent <t>2100</t> <t>Bioanalyzer.</t> The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.
2100 Bioanalyzer Instrument, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 112 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 93 stars, based on 112 article reviews
Price from $9.99 to $1999.99
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93/100 stars

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1) Product Images from "Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations"

Article Title: Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations

Journal: Oncotarget

doi: 10.18632/oncotarget.11796

Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.
Figure Legend Snippet: Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.

Techniques Used: Mutagenesis, Electrophoresis, Polymerase Chain Reaction, Synthesized, Isolation, Amplification, CTL Assay, Negative Control, RNA Sequencing Assay

2) Product Images from "Extraction of microRNAs from biological matrices with titanium dioxide nanofibers"

Article Title: Extraction of microRNAs from biological matrices with titanium dioxide nanofibers

Journal: Analytical and bioanalytical chemistry

doi: 10.1007/s00216-017-0649-3

Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000
Figure Legend Snippet: Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000

Techniques Used: RNA Extraction, Multiple Displacement Amplification

3) Product Images from "Extraction of microRNAs from biological matrices with titanium dioxide nanofibers"

Article Title: Extraction of microRNAs from biological matrices with titanium dioxide nanofibers

Journal: Analytical and bioanalytical chemistry

doi: 10.1007/s00216-017-0649-3

Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000
Figure Legend Snippet: Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000

Techniques Used: RNA Extraction, Multiple Displacement Amplification

4) Product Images from "An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)"

Article Title: An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

Journal: FEBS Open Bio

doi: 10.1002/2211-5463.12561

Electropherograms of total RNA from cassava obtained using our method showing 18S and 25S rRNA regions with RNA concentrations and RIN values; (A) to (C) correspond with RNA from leaves and storage roots, and (A) and (B) correspond with RNA from different stages of plant development (young and mature leaves). RNA were visualized in denaturing agarose gels stained with SYBR safe. RNA were analyzed using Agilent RNA 6000 Nano Assays in a 2100 Bioanalyzer (Agilent Technologies) and were then used for RNA sequencing.
Figure Legend Snippet: Electropherograms of total RNA from cassava obtained using our method showing 18S and 25S rRNA regions with RNA concentrations and RIN values; (A) to (C) correspond with RNA from leaves and storage roots, and (A) and (B) correspond with RNA from different stages of plant development (young and mature leaves). RNA were visualized in denaturing agarose gels stained with SYBR safe. RNA were analyzed using Agilent RNA 6000 Nano Assays in a 2100 Bioanalyzer (Agilent Technologies) and were then used for RNA sequencing.

Techniques Used: Staining, RNA Sequencing Assay

Electropherogram of sequencing libraries; the graph shows length distribution curves of sequencing libraries obtained using a low‐cost library construction protocol 18 . Curves were generated on a 2100 Bioanalyzer using a DNA 1000 chip (Agilent Technologies). The photograph was provided by Maria Irigoyen and Linda Walling, University of California, Riverside.
Figure Legend Snippet: Electropherogram of sequencing libraries; the graph shows length distribution curves of sequencing libraries obtained using a low‐cost library construction protocol 18 . Curves were generated on a 2100 Bioanalyzer using a DNA 1000 chip (Agilent Technologies). The photograph was provided by Maria Irigoyen and Linda Walling, University of California, Riverside.

Techniques Used: Sequencing, Generated, Chromatin Immunoprecipitation

5) Product Images from "Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes"

Article Title: Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

Journal: Scientific Reports

doi: 10.1038/srep41114

Depletion of rRNA from RNA samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of DNAse-treated RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.
Figure Legend Snippet: Depletion of rRNA from RNA samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of DNAse-treated RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.

Techniques Used: Isolation, Software, Real-time Polymerase Chain Reaction, Standard Deviation

Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
Figure Legend Snippet: Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.

Techniques Used: Isolation, Quantitation Assay, RNA HS Assay, Software, Fluorescence

6) Product Images from "High quality RNA extraction from Maqui berry for its application in next-generation sequencing"

Article Title: High quality RNA extraction from Maqui berry for its application in next-generation sequencing

Journal: SpringerPlus

doi: 10.1186/s40064-016-2906-x

Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of DNA fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using DNA 1000 chip (Agilent Technologies). For each sample three biological replicates were performed
Figure Legend Snippet: Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of DNA fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using DNA 1000 chip (Agilent Technologies). For each sample three biological replicates were performed

Techniques Used: Sequencing, Sample Prep, Generated, Chromatin Immunoprecipitation

Electrophoretogram of total RNA obtained with our new method. The 18S and 28S rRNA 25 regions are shown. RNA concentrations and RIN values are shown below. a green fruit. b red fruit. c blue fruit. RNA was analyzed with the Agilent RNA 6000 Nano Assay in a 2100 bioanalyzer (Agilent Technologies). Note that the output from our instrument is completely opposite from the English convention, therefore, it uses commas as an indicator of decimals, and periods to denote thousands. It is shown one result of the three RNA extraction obtained from the same tissue
Figure Legend Snippet: Electrophoretogram of total RNA obtained with our new method. The 18S and 28S rRNA 25 regions are shown. RNA concentrations and RIN values are shown below. a green fruit. b red fruit. c blue fruit. RNA was analyzed with the Agilent RNA 6000 Nano Assay in a 2100 bioanalyzer (Agilent Technologies). Note that the output from our instrument is completely opposite from the English convention, therefore, it uses commas as an indicator of decimals, and periods to denote thousands. It is shown one result of the three RNA extraction obtained from the same tissue

Techniques Used: RNA Extraction

7) Product Images from "The Dormancy Regulator DosR Controls Ribosome Stability in Hypoxic Mycobacteria *"

Article Title: The Dormancy Regulator DosR Controls Ribosome Stability in Hypoxic Mycobacteria *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M112.364851

Loss of DosR has a profound effect on ribosome and ribosomal RNA stability. Cultures of M. smegmatis mc 2 155 wild-type and the Δ dosR mutant were grown at 37 °C to mid-exponential phase ( A ), normoxic stationary phase ( B ), or hypoxic stationary phase ( C ). Cells were harvested, lysed, and ribosomes were isolated by ultracentrifugation and fractionated through a linear sucrose gradient (15–40%). Then the A 254 and refraction were determined per fraction and plotted. D and E , for ribosomal RNA stability experiments, cultures were grown to hypoxic stationary phase at 37 °C in LB. RNA was purified using the TRIzol reagent and analyzed with RNA Nano 6000 chips on an Agilent 2100 bioanalyzer. Traces shown are the average of three independent experiments and were normalized to account for chip variability.
Figure Legend Snippet: Loss of DosR has a profound effect on ribosome and ribosomal RNA stability. Cultures of M. smegmatis mc 2 155 wild-type and the Δ dosR mutant were grown at 37 °C to mid-exponential phase ( A ), normoxic stationary phase ( B ), or hypoxic stationary phase ( C ). Cells were harvested, lysed, and ribosomes were isolated by ultracentrifugation and fractionated through a linear sucrose gradient (15–40%). Then the A 254 and refraction were determined per fraction and plotted. D and E , for ribosomal RNA stability experiments, cultures were grown to hypoxic stationary phase at 37 °C in LB. RNA was purified using the TRIzol reagent and analyzed with RNA Nano 6000 chips on an Agilent 2100 bioanalyzer. Traces shown are the average of three independent experiments and were normalized to account for chip variability.

Techniques Used: Mutagenesis, Isolation, Purification, Chromatin Immunoprecipitation

Related Articles

Sequencing:

Article Title: Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations
Article Snippet: .. Amplified fragments were analyzed on the Agilent 2100 Bioanalyzer Instrument and by Sanger sequencing (McGill University and Genome Quebec Innovation Centre). .. ShRNA-mediated gene knockdown Lentivirus-mediated gene-specific small hairpin RNAs (shRNAs) were used to knockdown expression of 2 candidate driver genes: USP9X , and MED12 , in Jurkat (human T leukemia) cells.

Amplification:

Article Title: Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations
Article Snippet: .. Amplified fragments were analyzed on the Agilent 2100 Bioanalyzer Instrument and by Sanger sequencing (McGill University and Genome Quebec Innovation Centre). .. ShRNA-mediated gene knockdown Lentivirus-mediated gene-specific small hairpin RNAs (shRNAs) were used to knockdown expression of 2 candidate driver genes: USP9X , and MED12 , in Jurkat (human T leukemia) cells.

Chromatin Immunoprecipitation:

Article Title: The Dormancy Regulator DosR Controls Ribosome Stability in Hypoxic Mycobacteria *
Article Snippet: .. RNA integrity was assayed using the Agilent RNA 6000 Nano Chip kit (Agilent) and analyzed by a 2100 Bioanalyzer instrument (Agilent). ..

Article Title: Extraction of microRNAs from biological matrices with titanium dioxide nanofibers
Article Snippet: .. The chip was run on an Agilent 2100 Bioanalyzer Instrument using the Small RNA Analysis Kit with 1 μL of extraction sample following the protocol provided by Agilent. .. The commercial column extraction protocol that was followed was the optimized protocol provided by Life Technologies for cell lysate with the provided buffers.

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    Agilent technologies 2100 bioanalyzer instrument
    Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent <t>2100</t> <t>Bioanalyzer.</t> The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.
    2100 Bioanalyzer Instrument, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 140 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/2100 bioanalyzer instrument/product/Agilent technologies
    Average 93 stars, based on 140 article reviews
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    2100 bioanalyzer instrument - by Bioz Stars, 2020-07
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    Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.

    Journal: Oncotarget

    Article Title: Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations

    doi: 10.18632/oncotarget.11796

    Figure Lengend Snippet: Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.

    Article Snippet: Amplified fragments were analyzed on the Agilent 2100 Bioanalyzer Instrument and by Sanger sequencing (McGill University and Genome Quebec Innovation Centre).

    Techniques: Mutagenesis, Electrophoresis, Polymerase Chain Reaction, Synthesized, Isolation, Amplification, CTL Assay, Negative Control, RNA Sequencing Assay

    Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000

    Journal: Analytical and bioanalytical chemistry

    Article Title: Extraction of microRNAs from biological matrices with titanium dioxide nanofibers

    doi: 10.1007/s00216-017-0649-3

    Figure Lengend Snippet: Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000

    Article Snippet: The chip was run on an Agilent 2100 Bioanalyzer Instrument using the Small RNA Analysis Kit with 1 μL of extraction sample following the protocol provided by Agilent.

    Techniques: RNA Extraction, Multiple Displacement Amplification

    ( a ) Multiplex ligation-dependent genome amplification (MLGA), reaction scheme.  (I)  Genomic DNA is digested by restriction enzyme to generate targets with defined ends.  (II)  Each MLGA probe consists of two oligonucleotides, one selector oligo of 70–74 nt (green) and one general vector oligo of 34 nt (red). MLGA probe together with DNA-ligase forms circular DNA of target molecules after denaturation and hybridization.  (III)  To reduce background signal in the assay, undesirable, linear DNA is degraded by exonuclease I (Exo I).  (IV)  Multiplex PCR is facilitated by using universal primers that hybridize to a sequence in the vector. PCR products are analyzed using the Agilent Bioanalyzer 2100™ electrophoresis system. ( b ) Data from an MLGA set of 14 probes targeting loci on human chromosomes 13, 18, 21, X and Y. The upper graph shows the resulting elution diagrams from analyses of male and female DNA pools.

    Journal: Nucleic Acids Research

    Article Title: MLGA--a rapid and cost-efficient assay for gene copy-number analysis

    doi: 10.1093/nar/gkm651

    Figure Lengend Snippet: ( a ) Multiplex ligation-dependent genome amplification (MLGA), reaction scheme. (I) Genomic DNA is digested by restriction enzyme to generate targets with defined ends. (II) Each MLGA probe consists of two oligonucleotides, one selector oligo of 70–74 nt (green) and one general vector oligo of 34 nt (red). MLGA probe together with DNA-ligase forms circular DNA of target molecules after denaturation and hybridization. (III) To reduce background signal in the assay, undesirable, linear DNA is degraded by exonuclease I (Exo I). (IV) Multiplex PCR is facilitated by using universal primers that hybridize to a sequence in the vector. PCR products are analyzed using the Agilent Bioanalyzer 2100™ electrophoresis system. ( b ) Data from an MLGA set of 14 probes targeting loci on human chromosomes 13, 18, 21, X and Y. The upper graph shows the resulting elution diagrams from analyses of male and female DNA pools.

    Article Snippet: Temperature cycling was performed as follows: 37° C for 30 min, 95° C for 5 min followed by 30 cycles of 95° C 15 s, 55° C 30 s and 72° C for 60 s followed by 72° C for 10 min. PCR products were analyzed using an Agilent Bioanalyzer 2100™ instrument and quantified using the Agilent 2100 expert software, version B.02.02.SI238.

    Techniques: Multiplex Assay, Ligation, Amplification, Plasmid Preparation, Hybridization, Polymerase Chain Reaction, Sequencing, Electrophoresis