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Kapa Biosystems kapa library quantification kit
Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at <t>DNA</t> regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using <t>Kapa,</t> Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.
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1) Product Images from "Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone"

Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone

Journal: Frontiers in Endocrinology

doi: 10.3389/fendo.2018.00034

Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.
Figure Legend Snippet: Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

Techniques Used: RNA Sequencing Assay, Cell Culture, Chromatin Immunoprecipitation, Amplification, Purification, Sequencing

2) Product Images from "Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone"

Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone

Journal: Frontiers in Endocrinology

doi: 10.3389/fendo.2018.00034

Schematic of the study. (A) Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) workflow. Following treatment with pulses of gonadotropin-releasing hormone (GnRH), LβT2 cells cultured in coverslips placed in racks [see in Ref. ( 9 )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.
Figure Legend Snippet: Schematic of the study. (A) Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) workflow. Following treatment with pulses of gonadotropin-releasing hormone (GnRH), LβT2 cells cultured in coverslips placed in racks [see in Ref. ( 9 )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

Techniques Used: Next-Generation Sequencing, Cell Culture, RNA Sequencing Assay, Chromatin Immunoprecipitation, Amplification, Purification, Sequencing

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Amplification:

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Synthesized:

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Blocking Assay:

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Real-time Polymerase Chain Reaction:

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Article Title: REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ
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Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
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Random Hexamer Labeling:

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Article Snippet: The first-strand cDNA of the mRNA fragments was synthe sized using reverse transcriptase and random hexamer primers. .. The libraries were quantified using a KAPA library quantification kit (KAPA Biosystems, South Africa) in an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

Expressing:

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Modification:

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Hybridization:

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Flow Cytometry:

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Ligation:

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Generated:

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Sequencing:

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Article Title: A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets
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Article Title: Transcriptome profiling of Plasmodium vivax in Saimiri monkeys identifies potential ligands for invasion
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Cellular Antioxidant Activity Assay:

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ChIP-sequencing:

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Multiplexing:

Article Title: REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ
Article Snippet: Fragmented cDNAs were run on a SPRI-TE library construction system (Beckman Coulter, Fullerton, CA, USA), and during the adaptor ligation step, uniquely indexed NEXTflex adapters (Bioo Scientific, Austin, TX, USA) were used for each of the samples to allow for multiplexing. .. The purified libraries were quantified using a Kapa library quantification kit (KAPA biosystems).

Article Title: Transcriptome profiling of Plasmodium vivax in Saimiri monkeys identifies potential ligands for invasion
Article Snippet: Briefly, mRNA was purified by poly(A) selection from 600 ng of total RNA and then fragmented for 8 min at 94 °C. cDNA was generated with random hexamers, and indexing adapters were added to facilitate multiplexing sequencing. .. Purified libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems) and the CFX96 Real-Time PCR Detection System (Bio-Rad), and were combined in equimolar amounts for sequencing on the HiSeq 2500 instrument.

Nucleic Acid Electrophoresis:

Article Title: Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage
Article Snippet: Amplicons were then purified and analyzed by gel electrophoresis and indexed using Nextera XT P5 and P7 index sequences for Illumina sequencing according to the manufacturer’s instructions (ten cycles). .. Gel-purified, indexed libraries were quantitated using the KAPA library quantification kit (Kapa Biosystems) performed on an Applied Biosystems 7500 Fast real-time PCR machine.

RNA Sequencing Assay:

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Article Title: REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ
Article Snippet: Paragraph title: Gene expression analysis, RNA-seq library construction and sequencing ... The purified libraries were quantified using a Kapa library quantification kit (KAPA biosystems).

Article Title: A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets
Article Snippet: Paragraph title: RNA sequencing (RNAseq) sample preparation ... Molarity of the final pool was precisely quantified by qPCR with KAPA Library Quantification kit (Kapa Biosystems) and CFX96 Touch Real-Time PCR.

Isolation:

Article Title: The chromatin remodeling factor CHD7 controls cerebellar development by regulating reelin expression
Article Snippet: Intact nuclei were isolated (EZ Prep Nuclear Isolation Kit, Sigma-Aldrich) from 50,000 freshly isolated GCps of each genotype, and ATAC-Seq libraries were produced as previously described ( ). .. Library quality was assessed on a 2100 Bioanalyzer and quantified using the KAPA library quantification kit (Kapa Biosystems).

Mouse Assay:

Article Title: The chromatin remodeling factor CHD7 controls cerebellar development by regulating reelin expression
Article Snippet: GCps were purified from P7 mice as described above. .. Library quality was assessed on a 2100 Bioanalyzer and quantified using the KAPA library quantification kit (Kapa Biosystems).

Polymerase Chain Reaction:

Article Title: An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene
Article Snippet: The enrichment and the barcoding of the purified di-tagged cDNAs were done with 15 cycles of PCR. .. The library size was determined with a 2100 Bioanalyzer Instrument (Agilent Technologies). qPCR quantifications were done with a Kapa Library quantification Kit (Kapa Biosystems).

Article Title: Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies
Article Snippet: After GEM clean up, GEM-RT products were subjected to two rounds of 14 PCR cycles using custom primers for rat and mouse, and 10x human BCR primers (10x Genomics, Pleasanton, CA) for human, followed by SPRIselect (Beckman Coulter, Brea, CA) beads clean up. .. Single-cell BCR V(D)J Libraries were prepared following the manufacturer’s user guide (10x Genomics, Pleasanton, CA, CG000086_SingleCellVDJReagentKitsUserGuide_RevB), and profiled using the Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA) and quantified with Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA).

Article Title: REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ
Article Snippet: Adapter-ligated libraries were enriched by PCR using a KAPA library amplification kit (KAPA biosystems, Wilmington, MA) (1 cycle at 98°C for 45 s; 7 cycles of 98°C for 15 s, 65°C for 30 s and 72°C for 30 s; 1 cycle at 72°C for 1 min) and purified with AmpureXP beads (Beckman Coulter). .. The purified libraries were quantified using a Kapa library quantification kit (KAPA biosystems).

Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
Article Snippet: PCR amplification was performed using Nextera PCR primers. .. Libraries were purified with AMPure beads and then quantified using a KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent) and sequenced on an Illumina HiSeq 2500 to > 164M reads with 50 bp read length, paired-end.

Article Title: Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage
Article Snippet: Amplicons were directly used as templates for MiSeq adaption by second-round PCR amplification (20 cycles). .. Gel-purified, indexed libraries were quantitated using the KAPA library quantification kit (Kapa Biosystems) performed on an Applied Biosystems 7500 Fast real-time PCR machine.

Article Title: A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets
Article Snippet: 12 PCR cycles were set up to amplify and add barcodes to the libraries. .. Molarity of the final pool was precisely quantified by qPCR with KAPA Library Quantification kit (Kapa Biosystems) and CFX96 Touch Real-Time PCR.

Article Title: Transcriptome profiling of Plasmodium vivax in Saimiri monkeys identifies potential ligands for invasion
Article Snippet: The adapter-ligated cDNA products were enriched using 15 cycles of PCR, as specified in the user’s guide. .. Purified libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems) and the CFX96 Real-Time PCR Detection System (Bio-Rad), and were combined in equimolar amounts for sequencing on the HiSeq 2500 instrument.

Construct:

Article Title: Extracellular Vesicles Transfer the Receptor Programmed Death-1 in Rheumatoid Arthritis
Article Snippet: The small RNA library of EVs was constructed using Illumina TruSeq Small RNA Sample Prep Kit (Illumina) by adding 5 µl of total RNA as input. .. The size and purity of the cDNA libraries were validated on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent) and the concentration was quantified using KAPA Library Quantification Kit (KAPA biosystems).

Agarose Gel Electrophoresis:

Article Title: Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes
Article Snippet: ChIP-Seq libraries were size selected by resolving 300-400 bp products on a 2% agarose gel, gel purified on MinElute gel extraction columns (Qiagen: 28604). .. Final concentrations for all libraries were quantified using the Qubit fluorimeter (Life Technologies), Agilent 2100 Bioanalyzer, and by KAPA library quantification kit (Kapa Biosystems: KK4408) prior to sequencing.

Article Title: Comparison of 16S rDNA Next Sequencing of Microbiome Communities From Post-scalder and Post-picker Stages in Three Different Commercial Poultry Plants Processing Three Classes of Broilers
Article Snippet: Confirmation of amplicon presence and relative size was conducted via a 1% agarose gel. .. The library was pooled and assessed for purity and concentration was evaluated via quantitative polymerase chain reaction (qPCR) using the standard protocol from the KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA, United States).

Purification:

Article Title: The chromatin remodeling factor CHD7 controls cerebellar development by regulating reelin expression
Article Snippet: GCps were purified from P7 mice as described above. .. Library quality was assessed on a 2100 Bioanalyzer and quantified using the KAPA library quantification kit (Kapa Biosystems).

Article Title: Circulating Tumor DNA Mutation Profiling by Targeted Next Generation Sequencing Provides Guidance for Personalized Treatments in Multiple Cancer Types
Article Snippet: .. The post-capture amplified library was purified by Agencourt AMPure XP beads and quantified by qPCR using the KAPA Library Quantification kit (KAPA Biosystems). .. Library fragment size was determined by the Agilent Technologies 2100 Bioanalyzer.

Article Title: Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes
Article Snippet: ChIP-Seq libraries were size selected by resolving 300-400 bp products on a 2% agarose gel, gel purified on MinElute gel extraction columns (Qiagen: 28604). .. Final concentrations for all libraries were quantified using the Qubit fluorimeter (Life Technologies), Agilent 2100 Bioanalyzer, and by KAPA library quantification kit (Kapa Biosystems: KK4408) prior to sequencing.

Article Title: An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene
Article Snippet: The enrichment and the barcoding of the purified di-tagged cDNAs were done with 15 cycles of PCR. .. The library size was determined with a 2100 Bioanalyzer Instrument (Agilent Technologies). qPCR quantifications were done with a Kapa Library quantification Kit (Kapa Biosystems).

Article Title: Extracellular Vesicles Transfer the Receptor Programmed Death-1 in Rheumatoid Arthritis
Article Snippet: Paragraph title: RNA Purification, Small RNA Library Preparation, and Sequencing ... The size and purity of the cDNA libraries were validated on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent) and the concentration was quantified using KAPA Library Quantification Kit (KAPA biosystems).

Article Title: REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ
Article Snippet: .. The purified libraries were quantified using a Kapa library quantification kit (KAPA biosystems). .. The libraries were loaded on cBot (Illumina, San Diego, CA, USA) at final concentration of 10 pM to perform cluster generation, followed by 2 × 76 bp sequencing on HiSeq 2000 (Illumina).

Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
Article Snippet: .. Libraries were purified with AMPure beads and then quantified using a KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent) and sequenced on an Illumina HiSeq 2500 to > 164M reads with 50 bp read length, paired-end. ..

Article Title: Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage
Article Snippet: Amplicons were then purified and analyzed by gel electrophoresis and indexed using Nextera XT P5 and P7 index sequences for Illumina sequencing according to the manufacturer’s instructions (ten cycles). .. Gel-purified, indexed libraries were quantitated using the KAPA library quantification kit (Kapa Biosystems) performed on an Applied Biosystems 7500 Fast real-time PCR machine.

Article Title: Transcriptome profiling of Plasmodium vivax in Saimiri monkeys identifies potential ligands for invasion
Article Snippet: .. Purified libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems) and the CFX96 Real-Time PCR Detection System (Bio-Rad), and were combined in equimolar amounts for sequencing on the HiSeq 2500 instrument. .. The libraries were sequenced using a paired-end run (2 × 75) with Rapid v2 chemistry (Illumina).

Chromatin Immunoprecipitation:

Article Title: Extracellular Vesicles Transfer the Receptor Programmed Death-1 in Rheumatoid Arthritis
Article Snippet: .. The size and purity of the cDNA libraries were validated on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent) and the concentration was quantified using KAPA Library Quantification Kit (KAPA biosystems). .. The libraries were purified in the size range of 140–160 bp by Pippin Prep (Sage Science), and then pooled as required, to be sequenced on the Illumina HiSeq 2000 instrument by Beijing Genomics Institute, China.

Article Title: Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies
Article Snippet: Gel Beads-in-Emulsion (GEMs) were formed in channels of a chip in the 10x Chromium instrument, and then collected into an Eppendorf plate for GEM reverse transcription (GEM-RT) reaction. .. Single-cell BCR V(D)J Libraries were prepared following the manufacturer’s user guide (10x Genomics, Pleasanton, CA, CG000086_SingleCellVDJReagentKitsUserGuide_RevB), and profiled using the Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA) and quantified with Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA).

Article Title: A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets
Article Snippet: RNA quality was checked using Agilent pico chip (Agilent Technologies). .. Molarity of the final pool was precisely quantified by qPCR with KAPA Library Quantification kit (Kapa Biosystems) and CFX96 Touch Real-Time PCR.

Selection:

Article Title: Transcriptome profiling of Plasmodium vivax in Saimiri monkeys identifies potential ligands for invasion
Article Snippet: Briefly, mRNA was purified by poly(A) selection from 600 ng of total RNA and then fragmented for 8 min at 94 °C. cDNA was generated with random hexamers, and indexing adapters were added to facilitate multiplexing sequencing. .. Purified libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems) and the CFX96 Real-Time PCR Detection System (Bio-Rad), and were combined in equimolar amounts for sequencing on the HiSeq 2500 instrument.

Sample Prep:

Article Title: Extracellular Vesicles Transfer the Receptor Programmed Death-1 in Rheumatoid Arthritis
Article Snippet: The small RNA library of EVs was constructed using Illumina TruSeq Small RNA Sample Prep Kit (Illumina) by adding 5 µl of total RNA as input. .. The size and purity of the cDNA libraries were validated on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent) and the concentration was quantified using KAPA Library Quantification Kit (KAPA biosystems).

Article Title: A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets
Article Snippet: Paragraph title: RNA sequencing (RNAseq) sample preparation ... Molarity of the final pool was precisely quantified by qPCR with KAPA Library Quantification kit (Kapa Biosystems) and CFX96 Touch Real-Time PCR.

Next-Generation Sequencing:

Article Title: Circulating Tumor DNA Mutation Profiling by Targeted Next Generation Sequencing Provides Guidance for Personalized Treatments in Multiple Cancer Types
Article Snippet: The post-capture amplified library was purified by Agencourt AMPure XP beads and quantified by qPCR using the KAPA Library Quantification kit (KAPA Biosystems). .. The target-enriched library was then sequenced on Illumina MiSeq or HiSeq4000 NGS platforms (Illumina) according to the manufacturer’s instructions.

Incubation:

Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
Article Snippet: Cell pellets were resuspended in the transposase reaction mix [5 µl 2× TD buffer, 0.5 µl transposase (Illumina) and 4.5 µl nuclease-free water] and incubated at 37°C for 30 min. DNA from the transposase reaction was purified with a DNA Clean & Concentrator-5 Kit (Zymo Research). .. Libraries were purified with AMPure beads and then quantified using a KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent) and sequenced on an Illumina HiSeq 2500 to > 164M reads with 50 bp read length, paired-end.

Produced:

Article Title: The chromatin remodeling factor CHD7 controls cerebellar development by regulating reelin expression
Article Snippet: Intact nuclei were isolated (EZ Prep Nuclear Isolation Kit, Sigma-Aldrich) from 50,000 freshly isolated GCps of each genotype, and ATAC-Seq libraries were produced as previously described ( ). .. Library quality was assessed on a 2100 Bioanalyzer and quantified using the KAPA library quantification kit (Kapa Biosystems).

Concentration Assay:

Article Title: Extracellular Vesicles Transfer the Receptor Programmed Death-1 in Rheumatoid Arthritis
Article Snippet: .. The size and purity of the cDNA libraries were validated on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent) and the concentration was quantified using KAPA Library Quantification Kit (KAPA biosystems). .. The libraries were purified in the size range of 140–160 bp by Pippin Prep (Sage Science), and then pooled as required, to be sequenced on the Illumina HiSeq 2000 instrument by Beijing Genomics Institute, China.

Article Title: REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ
Article Snippet: The purified libraries were quantified using a Kapa library quantification kit (KAPA biosystems). .. The libraries were loaded on cBot (Illumina, San Diego, CA, USA) at final concentration of 10 pM to perform cluster generation, followed by 2 × 76 bp sequencing on HiSeq 2000 (Illumina).

Article Title: Comparison of 16S rDNA Next Sequencing of Microbiome Communities From Post-scalder and Post-picker Stages in Three Different Commercial Poultry Plants Processing Three Classes of Broilers
Article Snippet: .. The library was pooled and assessed for purity and concentration was evaluated via quantitative polymerase chain reaction (qPCR) using the standard protocol from the KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA, United States). .. The qPCR reactions were performed on an Eppendorf Mastercycler EP Gradient S (Eppendorf, Westbury, NY, United States) (R 2 = 0.999; Efficiency = 0.97).

High Throughput Screening Assay:

Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
Article Snippet: Paragraph title: Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing ... Libraries were purified with AMPure beads and then quantified using a KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent) and sequenced on an Illumina HiSeq 2500 to > 164M reads with 50 bp read length, paired-end.

Article Title: A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets
Article Snippet: Molarity of the final pool was precisely quantified by qPCR with KAPA Library Quantification kit (Kapa Biosystems) and CFX96 Touch Real-Time PCR. .. High-throughput sequencing was performed on an Illumina HiSeq 2500 system in Rapid Run mode, using two flow cells with paired-end 100-read length.

Gel Extraction:

Article Title: Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes
Article Snippet: ChIP-Seq libraries were size selected by resolving 300-400 bp products on a 2% agarose gel, gel purified on MinElute gel extraction columns (Qiagen: 28604). .. Final concentrations for all libraries were quantified using the Qubit fluorimeter (Life Technologies), Agilent 2100 Bioanalyzer, and by KAPA library quantification kit (Kapa Biosystems: KK4408) prior to sequencing.

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    Kapa Biosystems library quantification kit illumina universal
    Comparison of <t>Illumina</t> high-throughput sequencing and Illumina miRNA Bead Arrays v2 performance in thyroid tumor samples. Each dot represents the abundance of one mature miRNA in 1 of 20 samples in HTS (x-axis) and the fluorescent intensity of the corresponding spot on the microarray (y-axis) of all 20 samples. Expression values are based on normalized data, assuming perfect matching of microarray probe sequence and HTS sequence reads. The figure illustrates the saturation of microarray signals compared to the number of HTS reads and a lack of specificity of microarray probe hybridizations by the presence of fluorescent signal for miRNA targets without any HTS reads (x-axis position -∞). Because RPM normalization of low read counts generates visual artifact (column-like data structures between 0 and 5 RPM) we excluded all miRNAs with a very low abundance of one or two reads in individual samples. The correlation coefficient between the microarray and HTS data set is 0.67.
    Library Quantification Kit Illumina Universal, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/library quantification kit illumina universal/product/Kapa Biosystems
    Average 85 stars, based on 1 article reviews
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    library quantification kit illumina universal - by Bioz Stars, 2020-02
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    99
    Kapa Biosystems kapa library quantification kit
    Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at <t>DNA</t> regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using <t>Kapa,</t> Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.
    Kapa Library Quantification Kit, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 99/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kapa library quantification kit/product/Kapa Biosystems
    Average 99 stars, based on 77 article reviews
    Price from $9.99 to $1999.99
    kapa library quantification kit - by Bioz Stars, 2020-02
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    89
    Kapa Biosystems qpcr method
    Bland and Altman plot of differences between quantification methods <t>(Qubit</t> and <t>qPCR)</t> versus the mean of those measurements. Dashed lines represent the calculated limits of agreement (95%). In this plot, Qubit measurements were converted using a factor
    Qpcr Method, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 89/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qpcr method/product/Kapa Biosystems
    Average 89 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    qpcr method - by Bioz Stars, 2020-02
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    Image Search Results


    Comparison of Illumina high-throughput sequencing and Illumina miRNA Bead Arrays v2 performance in thyroid tumor samples. Each dot represents the abundance of one mature miRNA in 1 of 20 samples in HTS (x-axis) and the fluorescent intensity of the corresponding spot on the microarray (y-axis) of all 20 samples. Expression values are based on normalized data, assuming perfect matching of microarray probe sequence and HTS sequence reads. The figure illustrates the saturation of microarray signals compared to the number of HTS reads and a lack of specificity of microarray probe hybridizations by the presence of fluorescent signal for miRNA targets without any HTS reads (x-axis position -∞). Because RPM normalization of low read counts generates visual artifact (column-like data structures between 0 and 5 RPM) we excluded all miRNAs with a very low abundance of one or two reads in individual samples. The correlation coefficient between the microarray and HTS data set is 0.67.

    Journal: BMC Research Notes

    Article Title: Analysis options for high-throughput sequencing in miRNA expression profiling

    doi: 10.1186/1756-0500-7-144

    Figure Lengend Snippet: Comparison of Illumina high-throughput sequencing and Illumina miRNA Bead Arrays v2 performance in thyroid tumor samples. Each dot represents the abundance of one mature miRNA in 1 of 20 samples in HTS (x-axis) and the fluorescent intensity of the corresponding spot on the microarray (y-axis) of all 20 samples. Expression values are based on normalized data, assuming perfect matching of microarray probe sequence and HTS sequence reads. The figure illustrates the saturation of microarray signals compared to the number of HTS reads and a lack of specificity of microarray probe hybridizations by the presence of fluorescent signal for miRNA targets without any HTS reads (x-axis position -∞). Because RPM normalization of low read counts generates visual artifact (column-like data structures between 0 and 5 RPM) we excluded all miRNAs with a very low abundance of one or two reads in individual samples. The correlation coefficient between the microarray and HTS data set is 0.67.

    Article Snippet: The barcoded libraries were size restricted between 140 and 165 bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer.

    Techniques: Next-Generation Sequencing, Microarray, Expressing, Sequencing

    Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

    Journal: Frontiers in Endocrinology

    Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone

    doi: 10.3389/fendo.2018.00034

    Figure Lengend Snippet: Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

    Article Snippet: Libraries were purified with AMPure beads and then quantified using a KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent) and sequenced on an Illumina HiSeq 2500 to > 164M reads with 50 bp read length, paired-end.

    Techniques: RNA Sequencing Assay, Cell Culture, Chromatin Immunoprecipitation, Amplification, Purification, Sequencing

    Schematic of the study. (A) Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) workflow. Following treatment with pulses of gonadotropin-releasing hormone (GnRH), LβT2 cells cultured in coverslips placed in racks [see in Ref. ( 9 )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

    Journal: Frontiers in Endocrinology

    Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone

    doi: 10.3389/fendo.2018.00034

    Figure Lengend Snippet: Schematic of the study. (A) Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) workflow. Following treatment with pulses of gonadotropin-releasing hormone (GnRH), LβT2 cells cultured in coverslips placed in racks [see in Ref. ( 9 )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

    Article Snippet: Libraries were purified with AMPure beads and then quantified using a KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent) and sequenced on an Illumina HiSeq 2500 to > 164M reads with 50 bp read length, paired-end.

    Techniques: Next-Generation Sequencing, Cell Culture, RNA Sequencing Assay, Chromatin Immunoprecipitation, Amplification, Purification, Sequencing

    Bland and Altman plot of differences between quantification methods (Qubit and qPCR) versus the mean of those measurements. Dashed lines represent the calculated limits of agreement (95%). In this plot, Qubit measurements were converted using a factor

    Journal: Forensic science international. Genetics

    Article Title: Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq

    doi: 10.1016/j.fsigen.2014.05.007

    Figure Lengend Snippet: Bland and Altman plot of differences between quantification methods (Qubit and qPCR) versus the mean of those measurements. Dashed lines represent the calculated limits of agreement (95%). In this plot, Qubit measurements were converted using a factor

    Article Snippet: To assess the accuracy of our template quantification step, a subset of samples (n=92) was quantified by two methods, following the manufacture’s recommendations: 1) a dsDNA-specific fluorescent dye method (Qubit), and 2) a qPCR method (KAPA Biosystem library quantification kit).

    Techniques: Real-time Polymerase Chain Reaction