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Illumina Inc preparation kit
Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1960 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 1960 article reviews
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preparation kit - by Bioz Stars, 2020-02
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Amplification:

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: .. 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. The double-strand cDNA was performed followed by PCR amplification.

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. The fragmented cDNA was treated with end-repair, A-tailing, adapter ligation and 10 cycles of PCR amplification.

Synthesized:

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina). .. The fragmented poly(A) RNA enriched samples were subjected to cDNA synthesis using Illumina TruSeq preparation kit. cDNA was synthesized by reverse transcriptase (Super-Script II) using poly-dT and random hexamer primers.

Concentration Assay:

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: The DNA concentration was determined with the Quant-iT PicoGreen kit (Molecular Probes/Invitrogen, Carlsbad, CA, United States). .. Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions.

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: RNA was quantified with NanoDrop and Bioanalyzer, and ~1 μg of RNA in a concentration of 20 ng/μL was used for library construction. .. TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions.

Real-time Polymerase Chain Reaction:

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions. .. Libraries were quantified using Qubit dsDNA HS kit on a Qubit 2.0 fluorometer (Life technologies, Carlsbad, CA, United States) and KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, United States) according to the Illumina suggested protocol.

Article Title: SOX2 Drives Bronchial Dysplasia in a Novel Organotypic Model of Early Human Squamous Lung Cancer
Article Snippet: The TruSeq Stranded mRNA HT sample preparation kit (Illumina, Chesterford, UK) was used according to the manufacturer’s instructions. .. Libraries were quantified on a Tapestation DNA 1,000 Screen tape (Agilent, Cheadle, UK) and by quantitative PCR (qPCR) using a next-generation sequencing (NGS) Library Quantification Kit (KAPA Biosystems, London, UK) on an AriaMx qPCR system (Agilent).

Random Hexamer Labeling:

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina). .. The fragmented poly(A) RNA enriched samples were subjected to cDNA synthesis using Illumina TruSeq preparation kit. cDNA was synthesized by reverse transcriptase (Super-Script II) using poly-dT and random hexamer primers.

Article Title: Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Article Snippet: Sequencing libraries were produced using the Illumina mRNA sequencing sample preparation kit (Illumina, San Diego, USA), following the manufacturer's instructions. .. After reverse transcription to cDNA using random hexamer primers, end-repair and A-tailing of the double stranded cDNA was performed.

Expressing:

Article Title: CXCR2 Inhibition Combined with Sorafenib Improved Antitumor and Antiangiogenic Response in Preclinical Models of Ovarian Cancer
Article Snippet: .. Gene expression of ELR+ CXC chemokines Transcriptome sequencing was performed using the Illumina MiSeq sequencer and Illumina TruSeq RNA v2 sample preparation kit and protocols (Illumina, Inc.). ..

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods. .. All the RNA-Seq data has been deposited in the Gene Expression Omnibus under the accession number GSE69822 .

Genome Wide:

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: Genome-wide mRNA profiling was performed by RNA-Seq on WT MCF10a cells starved overnight then stimulated with 10 ng/ml EGF for 15, 40, 90, 180 and 300 min (Figure ). .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods.

Flow Cytometry:

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions. .. Each sample was barcoded with a unique sequence index tag, and pools of 12 different barcoded samples were loaded in 8 lanes of a single flow cell of Illumina HiScanSQ machine.

Ligation:

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. The fragmented cDNA was treated with end-repair, A-tailing, adapter ligation and 10 cycles of PCR amplification.

Generated:

Article Title: Genome Sequence of a Novel Enterococcus faecalis Sequence Type 922 Strain Isolated from a Door Handle in the Intensive Care Unit of a District Hospital in Durban, South Africa
Article Snippet: A paired-end library (2 × 300 bp) was prepared using an Illumina Nextera XT DNA sample preparation kit and sequenced on a MiSeq machine (Illumina, San Diego, CA, USA). .. The generated sequenced reads (2,003,064 reads) were quality assessed and trimmed using the next-generation sequencing (NGS) core tools in the CLC Genomics Workbench version 11.0.1 (CLC bio/Qiagen, Aarhus, Denmark).

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: .. Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. Briefly, the rRNA-depleted RNA was fragmented and reversed transcribed using Superscript II (Invitrogen, Carlsbad, CA, USA), followed by second-strand synthesis.

DNA Sequencing:

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: .. Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions. .. The libraries were evaluated on 2100 Bioanalyzer using High Sensitivity DNA kit (Agilent, Santa Clara, CA, United States) to estimate the library size.

Sequencing:

Article Title: CXCR2 Inhibition Combined with Sorafenib Improved Antitumor and Antiangiogenic Response in Preclinical Models of Ovarian Cancer
Article Snippet: .. Gene expression of ELR+ CXC chemokines Transcriptome sequencing was performed using the Illumina MiSeq sequencer and Illumina TruSeq RNA v2 sample preparation kit and protocols (Illumina, Inc.). ..

Article Title: Genome Sequence of a Novel Enterococcus faecalis Sequence Type 922 Strain Isolated from a Door Handle in the Intensive Care Unit of a District Hospital in Durban, South Africa
Article Snippet: Here, we present the emergence of sequence type 922 (ST922), a novel E. faecalis sequence type found in strain 2SIL2, isolated from a door handle in the intensive care unit of a district hospital in Durban, South Africa. .. A paired-end library (2 × 300 bp) was prepared using an Illumina Nextera XT DNA sample preparation kit and sequenced on a MiSeq machine (Illumina, San Diego, CA, USA).

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: .. Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina). .. 1μg of total RNA for each sample was used for poly(A) RNA selection using magnetic beads coated with poly-dT, followed by thermal fragmentation.

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: .. 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: Paragraph title: Extraction and Sequencing of Soil Genomic DNA ... Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions.

Article Title: Impact of “Raised without Antibiotics” Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance
Article Snippet: Paragraph title: Metagenomic sequencing. ... Libraries were prepared using the Illumina TruSeq DNA sample preparation kit (Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

Article Title: SOX2 Drives Bronchial Dysplasia in a Novel Organotypic Model of Early Human Squamous Lung Cancer
Article Snippet: Sample sequencing libraries were prepared from 200 ng of total RNA extracted from treated and control OTCs 4 days after the addition of doxycycline. .. The TruSeq Stranded mRNA HT sample preparation kit (Illumina, Chesterford, UK) was used according to the manufacturer’s instructions.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Paragraph title: Small RNA library preparation and sequencing ... Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively.

Article Title: Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Article Snippet: .. Sequencing libraries were produced using the Illumina mRNA sequencing sample preparation kit (Illumina, San Diego, USA), following the manufacturer's instructions. .. Briefly, 4 μg of total RNA was used as input for poly A+ selection, followed by metal-catalyzed fragmentation of the selected mRNA (peak of size distribution at ~240 nt).

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina). ..

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: Paragraph title: RNA library preparation and sequencing ... TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions.

DNA Extraction:

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: Extraction and Sequencing of Soil Genomic DNA Genomic DNA was extracted from 250 mg of soil obtained from each subsample (avoiding small pieces of roots) using the PowerLyzer® PowerSoil® DNA Isolation kit (MoBio Laboratories, Carlsbad, CA, United States) following the manufacturer’s instructions. .. Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions.

RNA Sequencing Assay:

Article Title: SOX2 Drives Bronchial Dysplasia in a Novel Organotypic Model of Early Human Squamous Lung Cancer
Article Snippet: Paragraph title: RNA sequencing ... The TruSeq Stranded mRNA HT sample preparation kit (Illumina, Chesterford, UK) was used according to the manufacturer’s instructions.

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: Genome-wide mRNA profiling was performed by RNA-Seq on WT MCF10a cells starved overnight then stimulated with 10 ng/ml EGF for 15, 40, 90, 180 and 300 min (Figure ). .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods.

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: Paragraph title: RNA-seq ... Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina).

Magnetic Beads:

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina). .. 1μg of total RNA for each sample was used for poly(A) RNA selection using magnetic beads coated with poly-dT, followed by thermal fragmentation.

Isolation:

Article Title: Genome Sequence of a Novel Enterococcus faecalis Sequence Type 922 Strain Isolated from a Door Handle in the Intensive Care Unit of a District Hospital in Durban, South Africa
Article Snippet: The 2SIL2 strain was isolated and confirmed as Enterococcus faecalis using Enterococcus selective agar base (Sigma-Aldrich, St. Louis, MO, USA) and an API 20 strep kit (bioMérieux, Marcy-l’Etoile, France). .. A paired-end library (2 × 300 bp) was prepared using an Illumina Nextera XT DNA sample preparation kit and sequenced on a MiSeq machine (Illumina, San Diego, CA, USA).

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: Paragraph title: Total RNA isolation and mRNA sequencing sample preparation ... Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina).

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: The DNA isolated from each of the three soil subsamples per mesocosm was then pooled and concentrated using the Genomic DNA Clean and Concentrator kit (Zymo Research Corporation, Irvine, CA, United States), constituting a single DNA sample per mesocosm. .. Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Firstly, the total RNA was isolated from gill tissues with TRIzol reagent (Invitrogen), and the RNA of 15–40 nt was purified by the 15% Polyacrylamide gel. .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively.

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: RNA-seq BMDM from LysM-Cre:NELF-B wt/wt (WT) and/or LysM-Cre:NELF-B fl/fl (NELF-B KO) mice were treated as indicated in individual figure legends (vehicle, LPS, LPS + Dex for 1 hr) and RNA was isolated using Qiagen RNA-easy kit. .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina).

Multiplex Assay:

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Purification:

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: The total RNA isolation and sequencing library preparation from IR-induced senescent and proliferating IMR90 cells was performed as follows: total RNA was isolated using Qiazol Lysis Reagent (Qiagen) and purified with the miRNeasy kit (Qiagen). .. Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina).

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Firstly, the total RNA was isolated from gill tissues with TRIzol reagent (Invitrogen), and the RNA of 15–40 nt was purified by the 15% Polyacrylamide gel. .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively.

Article Title: N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
Article Snippet: .. The purified RNA sample (IP) as well as the input PAR-CLIP RNA sample (Input control) were used for library construction by Truseq small RNA sample preparation kit (Illumina). .. Libraries were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012, Illumina) according to the manufacturer's instructions, and then sequenced by Illumina Hiseq2000 with single end 50-bp read length.

Polymerase Chain Reaction:

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: The concentrated DNA was resuspended in 20 μL of PCR water, and both purity and quality of the genomic DNA were assessed via spectrophotometry on a NanoDrop apparatus (NanoDrop® ND-1000 NanoDrop Technologies, Inc., Wilmington, DE, United States) to determine the absorbance at the following wavelengths: 230, 260, 280, and 320 nm. .. Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. The double-strand cDNA was performed followed by PCR amplification.

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. The fragmented cDNA was treated with end-repair, A-tailing, adapter ligation and 10 cycles of PCR amplification.

cDNA Library Assay:

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. Then these small RNAs were ligated sequentially to 5′ and 3′ adapters and used SuperScript II Reverse Transcriptase (Life Technologies) to synthesize the first-strand cDNA.

Mouse Assay:

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: RNA-seq BMDM from LysM-Cre:NELF-B wt/wt (WT) and/or LysM-Cre:NELF-B fl/fl (NELF-B KO) mice were treated as indicated in individual figure legends (vehicle, LPS, LPS + Dex for 1 hr) and RNA was isolated using Qiagen RNA-easy kit. .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina).

RNA Extraction:

Article Title: Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Article Snippet: Paragraph title: RNA extraction and sequencing ... Sequencing libraries were produced using the Illumina mRNA sequencing sample preparation kit (Illumina, San Diego, USA), following the manufacturer's instructions.

Selection:

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina). .. 1μg of total RNA for each sample was used for poly(A) RNA selection using magnetic beads coated with poly-dT, followed by thermal fragmentation.

Article Title: Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Article Snippet: Sequencing libraries were produced using the Illumina mRNA sequencing sample preparation kit (Illumina, San Diego, USA), following the manufacturer's instructions. .. Briefly, 4 μg of total RNA was used as input for poly A+ selection, followed by metal-catalyzed fragmentation of the selected mRNA (peak of size distribution at ~240 nt).

Sample Prep:

Article Title: CXCR2 Inhibition Combined with Sorafenib Improved Antitumor and Antiangiogenic Response in Preclinical Models of Ovarian Cancer
Article Snippet: .. Gene expression of ELR+ CXC chemokines Transcriptome sequencing was performed using the Illumina MiSeq sequencer and Illumina TruSeq RNA v2 sample preparation kit and protocols (Illumina, Inc.). ..

Article Title: Genome Sequence of a Novel Enterococcus faecalis Sequence Type 922 Strain Isolated from a Door Handle in the Intensive Care Unit of a District Hospital in Durban, South Africa
Article Snippet: .. A paired-end library (2 × 300 bp) was prepared using an Illumina Nextera XT DNA sample preparation kit and sequenced on a MiSeq machine (Illumina, San Diego, CA, USA). .. The generated sequenced reads (2,003,064 reads) were quality assessed and trimmed using the next-generation sequencing (NGS) core tools in the CLC Genomics Workbench version 11.0.1 (CLC bio/Qiagen, Aarhus, Denmark).

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: .. Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina). .. 1μg of total RNA for each sample was used for poly(A) RNA selection using magnetic beads coated with poly-dT, followed by thermal fragmentation.

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: .. 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: .. Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions. .. The libraries were evaluated on 2100 Bioanalyzer using High Sensitivity DNA kit (Agilent, Santa Clara, CA, United States) to estimate the library size.

Article Title: Impact of “Raised without Antibiotics” Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance
Article Snippet: .. Libraries were prepared using the Illumina TruSeq DNA sample preparation kit (Illumina, Inc., San Diego, CA) according to the manufacturer's instructions. .. Next-generation sequencing was performed on the Illumina NextSeq 500 platform (Illumina, Inc.).

Article Title: SOX2 Drives Bronchial Dysplasia in a Novel Organotypic Model of Early Human Squamous Lung Cancer
Article Snippet: .. The TruSeq Stranded mRNA HT sample preparation kit (Illumina, Chesterford, UK) was used according to the manufacturer’s instructions. ..

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. Then these small RNAs were ligated sequentially to 5′ and 3′ adapters and used SuperScript II Reverse Transcriptase (Life Technologies) to synthesize the first-strand cDNA.

Article Title: A Genome-Wide Regulatory Framework Identifies Maize PericarpColor1 Controlled Genes [C] Controlled Genes [C] [W]
Article Snippet: .. The preparation of mRNA-Seq libraries was performedaccording to instructions from the Illumina mRNA-Seq sample preparation kit(RS-100-0801 Illumina). .. Total RNA extracted from P1-rr and P1-ww pericarps harvested at 14 and 25 and silks harvested 1 to 2 dpostemergence were treated with DNaseI (Promega) twice to ensure no genomic DNAcontamination.

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods. .. All the RNA-Seq data has been deposited in the Gene Expression Omnibus under the accession number GSE69822 .

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: .. Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. Briefly, the rRNA-depleted RNA was fragmented and reversed transcribed using Superscript II (Invitrogen, Carlsbad, CA, USA), followed by second-strand synthesis.

Article Title: N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
Article Snippet: .. The purified RNA sample (IP) as well as the input PAR-CLIP RNA sample (Input control) were used for library construction by Truseq small RNA sample preparation kit (Illumina). .. Libraries were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012, Illumina) according to the manufacturer's instructions, and then sequenced by Illumina Hiseq2000 with single end 50-bp read length.

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina). ..

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: .. TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions. .. Each sample was barcoded with a unique sequence index tag, and pools of 12 different barcoded samples were loaded in 8 lanes of a single flow cell of Illumina HiScanSQ machine.

Ethanol Precipitation:

Article Title: A Genome-Wide Regulatory Framework Identifies Maize PericarpColor1 Controlled Genes [C] Controlled Genes [C] [W]
Article Snippet: The preparation of mRNA-Seq libraries was performedaccording to instructions from the Illumina mRNA-Seq sample preparation kit(RS-100-0801 Illumina). .. The poly(A)-enriched mRNA wasfragmented by heating at 94°C for 5 min in fragmentation buffer suppliedby Illumina, followed by ethanol precipitation.

Article Title: N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
Article Snippet: After that, the RNA was eluted by 1 hour incubation with 20 μl elution buffer (1× IP buffer and 6.7 mM m6 A, Sigma-Aldrich) under gentle shaking conditions, and purified by ethanol precipitation. .. The purified RNA sample (IP) as well as the input PAR-CLIP RNA sample (Input control) were used for library construction by Truseq small RNA sample preparation kit (Illumina).

Next-Generation Sequencing:

Article Title: Genome Sequence of a Novel Enterococcus faecalis Sequence Type 922 Strain Isolated from a Door Handle in the Intensive Care Unit of a District Hospital in Durban, South Africa
Article Snippet: A paired-end library (2 × 300 bp) was prepared using an Illumina Nextera XT DNA sample preparation kit and sequenced on a MiSeq machine (Illumina, San Diego, CA, USA). .. The generated sequenced reads (2,003,064 reads) were quality assessed and trimmed using the next-generation sequencing (NGS) core tools in the CLC Genomics Workbench version 11.0.1 (CLC bio/Qiagen, Aarhus, Denmark).

Article Title: Impact of “Raised without Antibiotics” Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance
Article Snippet: Libraries were prepared using the Illumina TruSeq DNA sample preparation kit (Illumina, Inc., San Diego, CA) according to the manufacturer's instructions. .. Next-generation sequencing was performed on the Illumina NextSeq 500 platform (Illumina, Inc.).

Article Title: SOX2 Drives Bronchial Dysplasia in a Novel Organotypic Model of Early Human Squamous Lung Cancer
Article Snippet: The TruSeq Stranded mRNA HT sample preparation kit (Illumina, Chesterford, UK) was used according to the manufacturer’s instructions. .. Libraries were quantified on a Tapestation DNA 1,000 Screen tape (Agilent, Cheadle, UK) and by quantitative PCR (qPCR) using a next-generation sequencing (NGS) Library Quantification Kit (KAPA Biosystems, London, UK) on an AriaMx qPCR system (Agilent).

Incubation:

Article Title: Genome Sequence of a Novel Enterococcus faecalis Sequence Type 922 Strain Isolated from a Door Handle in the Intensive Care Unit of a District Hospital in Durban, South Africa
Article Snippet: It was streaked onto a tryptic soy agar (TSA) (Sigma-Aldrich) plate and incubated at 37°C for 24 h. Following incubation, genomic DNA was extracted from 1 CFU of a pure culture of the isolate using the GenElute bacterial genomic DNA kit (Sigma-Aldrich). .. A paired-end library (2 × 300 bp) was prepared using an Illumina Nextera XT DNA sample preparation kit and sequenced on a MiSeq machine (Illumina, San Diego, CA, USA).

Article Title: N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
Article Snippet: After that, the RNA was eluted by 1 hour incubation with 20 μl elution buffer (1× IP buffer and 6.7 mM m6 A, Sigma-Aldrich) under gentle shaking conditions, and purified by ethanol precipitation. .. The purified RNA sample (IP) as well as the input PAR-CLIP RNA sample (Input control) were used for library construction by Truseq small RNA sample preparation kit (Illumina).

Spectrophotometry:

Article Title: Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
Article Snippet: The concentrated DNA was resuspended in 20 μL of PCR water, and both purity and quality of the genomic DNA were assessed via spectrophotometry on a NanoDrop apparatus (NanoDrop® ND-1000 NanoDrop Technologies, Inc., Wilmington, DE, United States) to determine the absorbance at the following wavelengths: 230, 260, 280, and 320 nm. .. Eighteen DNA sequencing libraries were prepared using the Illumina Nextera sample preparation kit (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions.

Produced:

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods. .. All the RNA-Seq data has been deposited in the Gene Expression Omnibus under the accession number GSE69822 .

Article Title: Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Article Snippet: .. Sequencing libraries were produced using the Illumina mRNA sequencing sample preparation kit (Illumina, San Diego, USA), following the manufacturer's instructions. .. Briefly, 4 μg of total RNA was used as input for poly A+ selection, followed by metal-catalyzed fragmentation of the selected mRNA (peak of size distribution at ~240 nt).

Immunoprecipitation:

Article Title: N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
Article Snippet: PARCLIP-MeRIP experiment applied m6 A-antibody immunoprecipitation , , to the hnRNP C PAR-CLIP RNA samples. .. The purified RNA sample (IP) as well as the input PAR-CLIP RNA sample (Input control) were used for library construction by Truseq small RNA sample preparation kit (Illumina).

Lysis:

Article Title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging
Article Snippet: The total RNA isolation and sequencing library preparation from IR-induced senescent and proliferating IMR90 cells was performed as follows: total RNA was isolated using Qiazol Lysis Reagent (Qiagen) and purified with the miRNeasy kit (Qiagen). .. Total RNA enrichment for sequencing poly(A) RNAs was performed with the TruSeq mRNA sample preparation kit (Illumina).

Fluorescence In Situ Hybridization:

Article Title: Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Article Snippet: RNA extraction and sequencing Total RNA was extracted from each fish's kidneys using the column-based RNA extraction kit (Qiagen, Venlo, Netherlands). .. Sequencing libraries were produced using the Illumina mRNA sequencing sample preparation kit (Illumina, San Diego, USA), following the manufacturer's instructions.

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