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Illumina Inc cbot
Cbot, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 191 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 191 article reviews
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cbot - by Bioz Stars, 2020-02
99/100 stars

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Amplification:

Article Title: Confidence-based Somatic Mutation Evaluation and Prioritization
Article Snippet: Hybridized gDNA/RNA bait complexes where removed using streptavidin coated magnetic beads. gDNA/RNA bait complexes were washed and the RNA baits cleaved off during elution in SureSelect elution buffer leaving the captured adapter ligated, PCR enriched gDNA fragments. gDNA fragments were PCR amplified post capture using Herculase II DNA polymerase (Agilent) and SureSelect GA PCR Primers for 10 cycles. .. Exome enriched gDNA libraries were clustered on the cBot using Truseq SR cluster kit v2.5 using 7 pM and sequenced on the Illumina HiSeq2000 using Truseq SBS kit.

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles. .. Raw sequencing data was processed using the onboard SCS/RTA software yielding 36 bp reads for GAIIx data.

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: Amplified libraries were quantified on MultiNA (Shimadzu) using the DNA-500 kit (cat#292-27910-91). .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001).

Article Title: Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Article Snippet: .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. ..

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: Paragraph title: 2.3. Viral RNA Isolation, cDNA Library Preparation, Amplification and Sequencing ... Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

Article Title: Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation
Article Snippet: The samples were then amplified by 15 rounds of PCR and purified using an equivalent volume of AMPure XP Beads. .. Finally, 10 ng of the library was used to generate clusters with cBot using a TruSeq PE Cluster Kit (Illumina, San Diego, CA, USA) followed by two-way sequencing on an Illumina HiSeq™ 4000/MiSeq™.

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: .. Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina). .. De novo assembly and functional annotation analysis using Illumina sequencing After sequencing, raw reads were obtained (Accession nos: SRX2676842/SRR5381733 in the NCBI SRA database).

Article Title: Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders, et al. Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders
Article Snippet: .. The cDNA libraries were amplified and sequenced using cBot and HiSeq2000 (Illumina, San Diego, USA). .. The sequence images were converted with the Illumina BaseCaller software to bcl files, which were demultiplexed to FASTQ files with CASAVA version 1.8.2.

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. .. Single end reads of 100nt were generated for each sample using Illumina’s HiSeq2500v4.

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: A miRNA library was made from each RNA sample by 3library was made from each RNA sample by human genome ligation, reverse transcription, and PCR amplification. .. Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina). .. Single-end reads of 100 nt were generated for each sample using Illumina’s HiSeq2500v4.

Synthesized:

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: Then, cDNA was synthesized using the fragments as templates. .. Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina).

Quantitative RT-PCR:

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: Paragraph title: RNA isolation, qRT-PCR and Illumina next-generation sequencing ... Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Electrophoresis:

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: Purified DNA was fragmented by sonication using the BioRuptor (Diagenode), and this was confirmed by capillary electrophoresis on the MultiNA (Shimadzu) using the DNA-2500 kit (cat#292-27912-91). .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001).

Article Title: Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation
Article Snippet: The library was then retrieved and quantified using Qubit, 2% agarose electrophoresis, and a High-Sensitivity DNA chip to ensure the quality of the library. .. Finally, 10 ng of the library was used to generate clusters with cBot using a TruSeq PE Cluster Kit (Illumina, San Diego, CA, USA) followed by two-way sequencing on an Illumina HiSeq™ 4000/MiSeq™.

Article Title: A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome Presentation
Article Snippet: Automated capillary electrophoresis with the RNA 6000 Nano kit on an Agilent BioAnalyzer 2100 was used to measure RNA integrity. .. Paired-end cluster generation was performed on the cBot as described by the manufacturer (Illumina, San Diego, CA, USA).

Incubation:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: After incubation, chromatin pulled down by the Protein G-bound antibodies was washed and immediately cleaned up with the IPure kit (Diagenode, AL-100-0100). .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

Expressing:

Article Title: Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Article Snippet: The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. .. Cufflinks2.0.2 with the gencode-M6 mouse gene annotations was then used to perform differential expression analysis.

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. .. All sequence data are available from the Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1234229 ) under accession number GSE134229).

Modification:

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: Library preparation was performed using a minor modification of the Illumina protocol (Illumina, San Diego, CA, USA). .. Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Derivative Assay:

Article Title: Tumor-immune profiling of murine syngeneic tumor models as a framework to guide mechanistic studies and predict therapy response in distinct tumor microenvironments
Article Snippet: Library clustering was performed on a cBot with Illumina HiSeq PE Cluster kit (#PE-401-4001) and sequenced on an Illumina HiSeq1500 or HiSeq2500 to ~50 million PE 2 x 101bp reads. .. Reads were aligned to the mouse genome (NCBI37.p3/mm9) using the OSA2 algorithm and a gene model derived from NCBI RefSeq annotation release 106.

Flow Cytometry:

Article Title: Confidence-based Somatic Mutation Evaluation and Prioritization
Article Snippet: Adapter ligated gDNA fragments were enriched pre capture and flow cell specific sequences were added using Illumina PE PCR primers 1.0 and 2.0 and Herculase II polymerase (Agilent) using 4 PCR cycles. .. Exome enriched gDNA libraries were clustered on the cBot using Truseq SR cluster kit v2.5 using 7 pM and sequenced on the Illumina HiSeq2000 using Truseq SBS kit.

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001). .. Base calling was performed by the Illumina RTA software version 1.8.

Article Title: Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Article Snippet: .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. ..

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: .. Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina). .. De novo assembly and functional annotation analysis using Illumina sequencing After sequencing, raw reads were obtained (Accession nos: SRX2676842/SRR5381733 in the NCBI SRA database).

Article Title: The Raccoon Polyomavirus Genome and Tumor Antigen Transcription Are Stable and Abundant in Neuroglial Tumors
Article Snippet: .. Indexed libraries were pooled and loaded on the cBot for cluster generation on TruSeq paired-end flow cells, and paired-end sequencing (2 × 100 bp, paired-end; 4 libraries/lane) was performed with an Illumina HiSeq 2000 sequencing system (BGI@UC Davis Joint Genome Center) using standard Illumina kit reagents (TruSeq SBS kit v3-HS). .. Image processing, base calling, quality scoring (Phred), FASTQ file generation, and sample demultiplexing were executed by HiSeq control software with real-time analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina).

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. .. Single end reads of 100nt were generated for each sample using Illumina’s HiSeq2500v4.

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: .. Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina). .. Sequencing (50 cycles) was performed on a HiSeq 2500 system (Illumina) using the primer sequences listed in Table .

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina). .. Single-end reads of 100 nt were generated for each sample using Illumina’s HiSeq2500v4.

Ligation:

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then went through an end repair process, the addition of a single “A” base, and then ligation of the adapters. .. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: A miRNA library was made from each RNA sample by 3library was made from each RNA sample by human genome ligation, reverse transcription, and PCR amplification. .. Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Article Title: A critical analysis of the role of SNARE protein SEC22B in antigen cross-presentation
Article Snippet: The 3′ ends of the cDNA were adenylated for ligation of adapters, one of which contained a 6-nucleotide barcode unique to each sample allowing for sample pooling. .. Libraries were clustered on the cBot (Illumina) and sequenced 3 samples per lane on a 50 cycle paired end on a HiSeq 2500 (Illumina) in High Output mode using version 4 reagents according to manufacturer’s recommended protocols.

Generated:

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: .. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA). ..

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. .. Single end reads of 100nt were generated for each sample using Illumina’s HiSeq2500v4.

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina). .. Single-end reads of 100 nt were generated for each sample using Illumina’s HiSeq2500v4.

Sequencing:

Article Title: Confidence-based Somatic Mutation Evaluation and Prioritization
Article Snippet: Paragraph title: Library capture and sequencing ... Exome enriched gDNA libraries were clustered on the cBot using Truseq SR cluster kit v2.5 using 7 pM and sequenced on the Illumina HiSeq2000 using Truseq SBS kit.

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles. .. Raw sequencing data was processed using the onboard SCS/RTA software yielding 36 bp reads for GAIIx data.

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001). .. Base calling was performed by the Illumina RTA software version 1.8.

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: Paragraph title: 2.3. Viral RNA Isolation, cDNA Library Preparation, Amplification and Sequencing ... Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

Article Title: Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation
Article Snippet: .. Finally, 10 ng of the library was used to generate clusters with cBot using a TruSeq PE Cluster Kit (Illumina, San Diego, CA, USA) followed by two-way sequencing on an Illumina HiSeq™ 4000/MiSeq™. .. All the data have been registered in the NCBI Sequence Read Archive (SRA) database ( https://trace.ncbi.nlm.nih.gov/Traces/sra/ ) under GenBank accession number SRP155676 (SAMN09736012, SAMN09736013, SAMN09736014, SAMN09736015, SAMN09736016, SAMN09736017).

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: Paragraph title: cDNA library preparation and Illumina sequencing ... Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina).

Article Title: Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders, et al. Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders
Article Snippet: The cDNA libraries were amplified and sequenced using cBot and HiSeq2000 (Illumina, San Diego, USA). .. The sequence images were converted with the Illumina BaseCaller software to bcl files, which were demultiplexed to FASTQ files with CASAVA version 1.8.2.

Article Title: Tumor-immune profiling of murine syngeneic tumor models as a framework to guide mechanistic studies and predict therapy response in distinct tumor microenvironments
Article Snippet: Library clustering was performed on a cBot with Illumina HiSeq PE Cluster kit (#PE-401-4001) and sequenced on an Illumina HiSeq1500 or HiSeq2500 to ~50 million PE 2 x 101bp reads. .. Quality filters included a minimum sequencing base quality of Q20 and the exclusion of both non-paired reads and reads which map to multiple locations on the genome.

Article Title: The Raccoon Polyomavirus Genome and Tumor Antigen Transcription Are Stable and Abundant in Neuroglial Tumors
Article Snippet: .. Indexed libraries were pooled and loaded on the cBot for cluster generation on TruSeq paired-end flow cells, and paired-end sequencing (2 × 100 bp, paired-end; 4 libraries/lane) was performed with an Illumina HiSeq 2000 sequencing system (BGI@UC Davis Joint Genome Center) using standard Illumina kit reagents (TruSeq SBS kit v3-HS). .. Image processing, base calling, quality scoring (Phred), FASTQ file generation, and sample demultiplexing were executed by HiSeq control software with real-time analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina).

Article Title: A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome Presentation
Article Snippet: Sequencing was performed at the Medical University of South Carolina Genomic Center (Charleston, SC, USA). .. Paired-end cluster generation was performed on the cBot as described by the manufacturer (Illumina, San Diego, CA, USA).

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). cDNA (1 ng) was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA). .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane.

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina). .. Sequencing (50 cycles) was performed on a HiSeq 2500 system (Illumina) using the primer sequences listed in Table .

Article Title: A critical analysis of the role of SNARE protein SEC22B in antigen cross-presentation
Article Snippet: Paragraph title: RNA preparation and sequencing ... Libraries were clustered on the cBot (Illumina) and sequenced 3 samples per lane on a 50 cycle paired end on a HiSeq 2500 (Illumina) in High Output mode using version 4 reagents according to manufacturer’s recommended protocols.

Sonication:

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: Purified DNA was fragmented by sonication using the BioRuptor (Diagenode), and this was confirmed by capillary electrophoresis on the MultiNA (Shimadzu) using the DNA-2500 kit (cat#292-27912-91). .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001).

Binding Assay:

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: DNA was eluted from the Methyl-CpG Binding Domain-coupled magnetic beads with 2 M NaCl. .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001).

ChIP-sequencing:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: ChIP-sequencing libraries were prepared using the ChIP-Seq DNA sample preparation kit (Illumina, IP-102-1001) using an adapter oligo dilution of 1:25 for all samples. .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

Nucleic Acid Electrophoresis:

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200–500 bp in size. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina).

RNA Sequencing Assay:

Article Title: Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Article Snippet: Paragraph title: RNA-sequencing ... The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane.

Article Title: Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders, et al. Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders
Article Snippet: Paragraph title: 2.6.3. cDNA Library Preparation and RNA Seq ... The cDNA libraries were amplified and sequenced using cBot and HiSeq2000 (Illumina, San Diego, USA).

Article Title: Tumor-immune profiling of murine syngeneic tumor models as a framework to guide mechanistic studies and predict therapy response in distinct tumor microenvironments
Article Snippet: Paragraph title: RNA seq analysis of murine cell lines ... Library clustering was performed on a cBot with Illumina HiSeq PE Cluster kit (#PE-401-4001) and sequenced on an Illumina HiSeq1500 or HiSeq2500 to ~50 million PE 2 x 101bp reads.

Article Title: A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome Presentation
Article Snippet: Paragraph title: 2.8. Next Generation RiboZero RNA Sequencing and RNA-Seq Data Analysis ... Paired-end cluster generation was performed on the cBot as described by the manufacturer (Illumina, San Diego, CA, USA).

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: Paragraph title: RNA-sequencing ... The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane.

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: Small RNA sequencing (smRNA-seq) was first performed to identify plasma miRNAs and some other circulating small ncRNAs in six samples pooled from 29 high-risk healthy individuals (there were 30 samples originally, but technical failure occurred in case), 30 individuals with benign lesions and 30 patients with LAC. .. Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Magnetic Beads:

Article Title: Confidence-based Somatic Mutation Evaluation and Prioritization
Article Snippet: Cleanups were performed using 1.8× volume of AMPure XP magnetic beads (Agencourt). .. Exome enriched gDNA libraries were clustered on the cBot using Truseq SR cluster kit v2.5 using 7 pM and sequenced on the Illumina HiSeq2000 using Truseq SBS kit.

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: DNA was eluted from the Methyl-CpG Binding Domain-coupled magnetic beads with 2 M NaCl. .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001).

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: Briefly, mRNA was purified from 200 ng total RNA with oligo-dT magnetic beads and fragmented. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina).

Isolation:

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: Paragraph title: 2.3. Viral RNA Isolation, cDNA Library Preparation, Amplification and Sequencing ... Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: RNA was isolated from purified T cells using the RNeasy Mini kit (Qiagen, Valencia, CA). .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane.

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: Paragraph title: RNA isolation, qRT-PCR and Illumina next-generation sequencing ... Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Purification:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: Immune-enriched chromatin was further purified with phenol/chloroform/isoamylalcohol (25:24:1) and concentrated by ethanol precipitation. .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: Purified DNA was fragmented by sonication using the BioRuptor (Diagenode), and this was confirmed by capillary electrophoresis on the MultiNA (Shimadzu) using the DNA-2500 kit (cat#292-27912-91). .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001).

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, Waltham, MA, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to confirm the insert size and calculate the mole concentration. .. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

Article Title: Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation
Article Snippet: The samples were then amplified by 15 rounds of PCR and purified using an equivalent volume of AMPure XP Beads. .. Finally, 10 ng of the library was used to generate clusters with cBot using a TruSeq PE Cluster Kit (Illumina, San Diego, CA, USA) followed by two-way sequencing on an Illumina HiSeq™ 4000/MiSeq™.

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: Short fragments were purified and resolved with an EB buffer for end reparation and a single nucleotide. .. Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina).

Article Title: Tumor-immune profiling of murine syngeneic tumor models as a framework to guide mechanistic studies and predict therapy response in distinct tumor microenvironments
Article Snippet: RNA seq analysis of murine cell lines Cell line RNA was purified using the Qiagen RNeasy kit, QIAshredder spin columns, and DNase 1. .. Library clustering was performed on a cBot with Illumina HiSeq PE Cluster kit (#PE-401-4001) and sequenced on an Illumina HiSeq1500 or HiSeq2500 to ~50 million PE 2 x 101bp reads.

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: RNA was isolated from purified T cells using the RNeasy Mini kit (Qiagen, Valencia, CA). .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane.

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200–500 bp in size. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina).

Polymerase Chain Reaction:

Article Title: Confidence-based Somatic Mutation Evaluation and Prioritization
Article Snippet: Hybridized gDNA/RNA bait complexes where removed using streptavidin coated magnetic beads. gDNA/RNA bait complexes were washed and the RNA baits cleaved off during elution in SureSelect elution buffer leaving the captured adapter ligated, PCR enriched gDNA fragments. gDNA fragments were PCR amplified post capture using Herculase II DNA polymerase (Agilent) and SureSelect GA PCR Primers for 10 cycles. .. Exome enriched gDNA libraries were clustered on the cBot using Truseq SR cluster kit v2.5 using 7 pM and sequenced on the Illumina HiSeq2000 using Truseq SBS kit.

Article Title: Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation
Article Snippet: The samples were then amplified by 15 rounds of PCR and purified using an equivalent volume of AMPure XP Beads. .. Finally, 10 ng of the library was used to generate clusters with cBot using a TruSeq PE Cluster Kit (Illumina, San Diego, CA, USA) followed by two-way sequencing on an Illumina HiSeq™ 4000/MiSeq™.

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: Suitable cDNA fragments were selected for PCR amplification. .. Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina).

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: A miRNA library was made from each RNA sample by 3library was made from each RNA sample by human genome ligation, reverse transcription, and PCR amplification. .. Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200–500 bp in size. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina).

Immunoprecipitation:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: The unbound fraction of the immunoprecipitation reaction was used to validate the fragmentation on a 1% agarose gel. .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

cDNA Library Assay:

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: Paragraph title: 2.3. Viral RNA Isolation, cDNA Library Preparation, Amplification and Sequencing ... Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: Paragraph title: cDNA library preparation and Illumina sequencing ... Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina).

Article Title: Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders, et al. Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders
Article Snippet: Paragraph title: 2.6.3. cDNA Library Preparation and RNA Seq ... The cDNA libraries were amplified and sequenced using cBot and HiSeq2000 (Illumina, San Diego, USA).

Sample Prep:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: ChIP-sequencing libraries were prepared using the ChIP-Seq DNA sample preparation kit (Illumina, IP-102-1001) using an adapter oligo dilution of 1:25 for all samples. .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

Article Title: Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Article Snippet: Illumina-compatible library construction was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, California) per manufacturer’s protocols. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane.

Article Title: Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders, et al. Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders
Article Snippet: The library was prepared using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, USA) starting from 500 ng of total RNA. .. The cDNA libraries were amplified and sequenced using cBot and HiSeq2000 (Illumina, San Diego, USA).

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: The TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next-generation sequencing library construction per manufacturer’s protocols. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina).

Chloramphenicol Acetyltransferase Assay:

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: .. Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (catFC-104-4001). .. Base calling was performed by the Illumina RTA software version 1.8.

Chromatin Immunoprecipitation:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) ... Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

Article Title: Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation
Article Snippet: The library was then retrieved and quantified using Qubit, 2% agarose electrophoresis, and a High-Sensitivity DNA chip to ensure the quality of the library. .. Finally, 10 ng of the library was used to generate clusters with cBot using a TruSeq PE Cluster Kit (Illumina, San Diego, CA, USA) followed by two-way sequencing on an Illumina HiSeq™ 4000/MiSeq™.

Software:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles. .. Raw sequencing data was processed using the onboard SCS/RTA software yielding 36 bp reads for GAIIx data.

Article Title: Non-referenced genome assembly from epigenomic short-read data
Article Snippet: Cluster generation was performed on cBot (Illumina) using version 4 Cluster Generation kits (single end sequencing, cat# GD-300-100), and the flow cell was processed on Genome Analyzer IIx (Illumina) with 151 cycles using version 4 SBS kits (cat#FC-104-4001). .. Base calling was performed by the Illumina RTA software version 1.8.

Article Title: Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders, et al. Effects of repeated long‐term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders
Article Snippet: The cDNA libraries were amplified and sequenced using cBot and HiSeq2000 (Illumina, San Diego, USA). .. The sequence images were converted with the Illumina BaseCaller software to bcl files, which were demultiplexed to FASTQ files with CASAVA version 1.8.2.

Article Title: The Raccoon Polyomavirus Genome and Tumor Antigen Transcription Are Stable and Abundant in Neuroglial Tumors
Article Snippet: Indexed libraries were pooled and loaded on the cBot for cluster generation on TruSeq paired-end flow cells, and paired-end sequencing (2 × 100 bp, paired-end; 4 libraries/lane) was performed with an Illumina HiSeq 2000 sequencing system (BGI@UC Davis Joint Genome Center) using standard Illumina kit reagents (TruSeq SBS kit v3-HS). .. Image processing, base calling, quality scoring (Phred), FASTQ file generation, and sample demultiplexing were executed by HiSeq control software with real-time analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina).

Article Title: A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome Presentation
Article Snippet: Paired-end cluster generation was performed on the cBot as described by the manufacturer (Illumina, San Diego, CA, USA). .. Demultiplexing from base calls was performed utilizing Illumina’s bcl2fastq software to generate FASTQ files.

Real-time Polymerase Chain Reaction:

Article Title: Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Article Snippet: An Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) and ABI 7500 real-time PCR machine (Applied Biosystems) were used to determine average molecular lengths. .. Then, qualified libraries were amplified on cBot to generate a cluster on flow cell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina), and paired-end clusters amplified using flow cell were sequenced on a HiSeq 2000 system (TruSeq SBS KIT-HS V3, Illumina).

Article Title: Tumor-immune profiling of murine syngeneic tumor models as a framework to guide mechanistic studies and predict therapy response in distinct tumor microenvironments
Article Snippet: The libraries were quantified and normalized by qPCR using KAPA Library Quantification Kit (ABI Prism #KK4835). .. Library clustering was performed on a cBot with Illumina HiSeq PE Cluster kit (#PE-401-4001) and sequenced on an Illumina HiSeq1500 or HiSeq2500 to ~50 million PE 2 x 101bp reads.

Article Title: A critical analysis of the role of SNARE protein SEC22B in antigen cross-presentation
Article Snippet: Final libraries were checked for quality and quantity by a TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (KK4835) (Kapa Biosystems,Wilmington MA) using manufacturer’s recommended protocols. .. Libraries were clustered on the cBot (Illumina) and sequenced 3 samples per lane on a 50 cycle paired end on a HiSeq 2500 (Illumina) in High Output mode using version 4 reagents according to manufacturer’s recommended protocols.

Agarose Gel Electrophoresis:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: The unbound fraction of the immunoprecipitation reaction was used to validate the fragmentation on a 1% agarose gel. .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

Ethanol Precipitation:

Article Title: Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration
Article Snippet: Immune-enriched chromatin was further purified with phenol/chloroform/isoamylalcohol (25:24:1) and concentrated by ethanol precipitation. .. Prepared samples were amplified onto flowcells using the Illumina Cluster Station or cBot per manufacturer protocol and sequenced on either the Illumina GAIIx for 36 cycles or the HiSeq 2000 platform for 50 cycles.

Next-Generation Sequencing:

Article Title: The Raccoon Polyomavirus Genome and Tumor Antigen Transcription Are Stable and Abundant in Neuroglial Tumors
Article Snippet: Paragraph title: Next-generation sequencing and data analysis. ... Indexed libraries were pooled and loaded on the cBot for cluster generation on TruSeq paired-end flow cells, and paired-end sequencing (2 × 100 bp, paired-end; 4 libraries/lane) was performed with an Illumina HiSeq 2000 sequencing system (BGI@UC Davis Joint Genome Center) using standard Illumina kit reagents (TruSeq SBS kit v3-HS).

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: Paragraph title: RNA isolation, qRT-PCR and Illumina next-generation sequencing ... Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina).

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: The TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next-generation sequencing library construction per manufacturer’s protocols. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina).

Random Hexamer Labeling:

Article Title: Targeting the gut microbiome to treat the osteoarthritis of obesity
Article Snippet: First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina).

Spectrophotometry:

Article Title: Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Article Snippet: RNA-sequencing RNA concentration was determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, Delaware) and RNA quality was assessed with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California). .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane.

Article Title: A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome Presentation
Article Snippet: Yield (absorbance at 260 nm) and purity (260/280 = 1.8–2.0, 260/230 ≥ 1.7) were assessed with a NanoDrop® (Thermo Scientific, Waltham, MA, USA) spectrophotometer. .. Paired-end cluster generation was performed on the cBot as described by the manufacturer (Illumina, San Diego, CA, USA).

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: Total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane.

Concentration Assay:

Article Title: Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Article Snippet: .. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. ..

Article Title: Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Article Snippet: Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, Waltham, MA, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to confirm the insert size and calculate the mole concentration. .. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. .. Single end reads of 100nt were generated for each sample using Illumina’s HiSeq2500v4.

Article Title: Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening
Article Snippet: .. Libraries were then pooled in batches of 12 samples of equal amounts and clustered with a concentration of 10.5 pmol in one lane for each single-read flow cell using cBot (Illumina). .. Sequencing (50 cycles) was performed on a HiSeq 2500 system (Illumina) using the primer sequences listed in Table .

FACS:

Article Title: Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life
Article Snippet: This created 6 unique pools of cells prior to FACs purification. .. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane.

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  • 99
    Illumina Inc illumina cbot
    Setting up lane-by-lane sequencing on an <t>Illumina</t> GAIIx a) <t>cBOT</t> cluster plate set up to cluster lanes 5–8. Lanes 1–4 have been removed using a razor blade and replaced with vials containing HSB. b) The TileSelection section of an XML recipe file for 4-lane sequencing of the flowcell clustered in a. Only lanes 5–8 will be imaged. c) Disconnecting the syringe-pumps. Once the manifold housing is removed, the plunger heads can be unscrewed from the motorized crossbar. Here, pumping has been inactivated on lanes 1 and 2. d) Pause-and-pulse reagent delivery method for reads longer than 40 nt. The left lane is active and the right lane is disconnected. Orange arrows represent flow of new reagent, green arrows represent movement of previous reagent, white circle represents a small air bubble remaining in the disconnected lane. i. During the initial pumping stage, reagent delivered from the inlet (bottom) may be contaminated by fluid from disconnected lanes as small bubbles expand due to negative pressure from the pump. ii. After pumping, a 5-second pause allows a small amount of the current reagent to back-fill through the inlet manifold as pressure equalizes in the system. iii. A 20 μL pulse then finishes delivery with homogenous reagent.
    Illumina Cbot, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 499 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    illumina cbot - by Bioz Stars, 2020-02
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    77
    Illumina Inc flowcell follow illumina cbot user guide
    DNA template and RNA transcript of HiTS-RAP. (A) Schematics of the DNA template used for HiTS-RAP and the resulting halted RNA transcript. DNA template encoding the RNA of interest (green) is flanked by the <t>Illumina</t> <t>flowcell</t> adaptor 1 (gray) and T7 RNA polymerase promoter (orange) upstream, and by the Illumina sequencing primer annealing site (purple), Tus-binding Ter site (red), and Illumina flowcell adaptor 2 downstream. Illumina flowcell adaptors 1 and 2 are required for cluster generation on Illumina GA flowcell. T7 RNA polymerase promoter is required for transcription of the RNA of interest. The Illumina sequencing primer is used for sequencing the DNA template of the RNA of interest and serves as a docking site for the T7 RNA polymerase when it is halted. Tus protein binds to Ter site and halts the transcribing RNA polymerase. Direction of transcription and sequencing are indicated by orange and purple arrows, respectively. Tus-bound Ter site that is non-permissive (halting) and permissive (read-through) to RNA polymerase are indicated by solid and open red triangles, respectively. The halted RNA transcript includes a triplet G derived from the T7 promoter, followed by the RNA of interest and some of the Illumina sequencing primer. The 3’-end of RNA transcript, indicated by a dashed line, is inaccessible. (B) Construction of DNA templates for HiTS-RAP. DNA template is constructed by PCR in two steps using 2 sets of nested oligos. Forward oligos introduce T7 promoter (step 1) and Illumina flowcell adaptor (step 2), whereas reverse oligos introduce Illumina sequencing primer (step 1), and Ter site and Illumina flowcell adaptor 2 (step 2). (C) Sequence of the HiTS-RAP DNA template for GFP aptamer. GFP aptamer encoding sequence is in green, and the rest of the sequences are colored as in (A). The transcription start site is indicated by +1 and a broken arrow. (D) Sequence of the halted RNA transcript from GFP aptamer template. Sequences are colored as in (C). Uppercase indicates the region of the halted RNA transcript that is accessible, and the lowercase indicates a region that is likely to be buried in T7 RNA polymerase and thus inaccessible by other proteins.
    Flowcell Follow Illumina Cbot User Guide, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Setting up lane-by-lane sequencing on an Illumina GAIIx a) cBOT cluster plate set up to cluster lanes 5–8. Lanes 1–4 have been removed using a razor blade and replaced with vials containing HSB. b) The TileSelection section of an XML recipe file for 4-lane sequencing of the flowcell clustered in a. Only lanes 5–8 will be imaged. c) Disconnecting the syringe-pumps. Once the manifold housing is removed, the plunger heads can be unscrewed from the motorized crossbar. Here, pumping has been inactivated on lanes 1 and 2. d) Pause-and-pulse reagent delivery method for reads longer than 40 nt. The left lane is active and the right lane is disconnected. Orange arrows represent flow of new reagent, green arrows represent movement of previous reagent, white circle represents a small air bubble remaining in the disconnected lane. i. During the initial pumping stage, reagent delivered from the inlet (bottom) may be contaminated by fluid from disconnected lanes as small bubbles expand due to negative pressure from the pump. ii. After pumping, a 5-second pause allows a small amount of the current reagent to back-fill through the inlet manifold as pressure equalizes in the system. iii. A 20 μL pulse then finishes delivery with homogenous reagent.

    Journal: BioTechniques

    Article Title: Lane-by-lane sequencing using Illumina’s Genome Analyzer II

    doi: 10.2144/000114032

    Figure Lengend Snippet: Setting up lane-by-lane sequencing on an Illumina GAIIx a) cBOT cluster plate set up to cluster lanes 5–8. Lanes 1–4 have been removed using a razor blade and replaced with vials containing HSB. b) The TileSelection section of an XML recipe file for 4-lane sequencing of the flowcell clustered in a. Only lanes 5–8 will be imaged. c) Disconnecting the syringe-pumps. Once the manifold housing is removed, the plunger heads can be unscrewed from the motorized crossbar. Here, pumping has been inactivated on lanes 1 and 2. d) Pause-and-pulse reagent delivery method for reads longer than 40 nt. The left lane is active and the right lane is disconnected. Orange arrows represent flow of new reagent, green arrows represent movement of previous reagent, white circle represents a small air bubble remaining in the disconnected lane. i. During the initial pumping stage, reagent delivered from the inlet (bottom) may be contaminated by fluid from disconnected lanes as small bubbles expand due to negative pressure from the pump. ii. After pumping, a 5-second pause allows a small amount of the current reagent to back-fill through the inlet manifold as pressure equalizes in the system. iii. A 20 μL pulse then finishes delivery with homogenous reagent.

    Article Snippet: Flowcells can be clustered on any desired number of lanes using the Illumina cBot, sequenced, stored, and then clustered again on remaining lanes without appreciable reduction in intensity, cluster density or accuracy of the run.

    Techniques: Sequencing, Flow Cytometry

    DNA template and RNA transcript of HiTS-RAP. (A) Schematics of the DNA template used for HiTS-RAP and the resulting halted RNA transcript. DNA template encoding the RNA of interest (green) is flanked by the Illumina flowcell adaptor 1 (gray) and T7 RNA polymerase promoter (orange) upstream, and by the Illumina sequencing primer annealing site (purple), Tus-binding Ter site (red), and Illumina flowcell adaptor 2 downstream. Illumina flowcell adaptors 1 and 2 are required for cluster generation on Illumina GA flowcell. T7 RNA polymerase promoter is required for transcription of the RNA of interest. The Illumina sequencing primer is used for sequencing the DNA template of the RNA of interest and serves as a docking site for the T7 RNA polymerase when it is halted. Tus protein binds to Ter site and halts the transcribing RNA polymerase. Direction of transcription and sequencing are indicated by orange and purple arrows, respectively. Tus-bound Ter site that is non-permissive (halting) and permissive (read-through) to RNA polymerase are indicated by solid and open red triangles, respectively. The halted RNA transcript includes a triplet G derived from the T7 promoter, followed by the RNA of interest and some of the Illumina sequencing primer. The 3’-end of RNA transcript, indicated by a dashed line, is inaccessible. (B) Construction of DNA templates for HiTS-RAP. DNA template is constructed by PCR in two steps using 2 sets of nested oligos. Forward oligos introduce T7 promoter (step 1) and Illumina flowcell adaptor (step 2), whereas reverse oligos introduce Illumina sequencing primer (step 1), and Ter site and Illumina flowcell adaptor 2 (step 2). (C) Sequence of the HiTS-RAP DNA template for GFP aptamer. GFP aptamer encoding sequence is in green, and the rest of the sequences are colored as in (A). The transcription start site is indicated by +1 and a broken arrow. (D) Sequence of the halted RNA transcript from GFP aptamer template. Sequences are colored as in (C). Uppercase indicates the region of the halted RNA transcript that is accessible, and the lowercase indicates a region that is likely to be buried in T7 RNA polymerase and thus inaccessible by other proteins.

    Journal: Nature protocols

    Article Title: Quantitative Assessment of RNA-Protein Interactions with High Throughput Sequencing - RNA Affinity Profiling (HiTS-RAP)

    doi: 10.1038/nprot.2015.074

    Figure Lengend Snippet: DNA template and RNA transcript of HiTS-RAP. (A) Schematics of the DNA template used for HiTS-RAP and the resulting halted RNA transcript. DNA template encoding the RNA of interest (green) is flanked by the Illumina flowcell adaptor 1 (gray) and T7 RNA polymerase promoter (orange) upstream, and by the Illumina sequencing primer annealing site (purple), Tus-binding Ter site (red), and Illumina flowcell adaptor 2 downstream. Illumina flowcell adaptors 1 and 2 are required for cluster generation on Illumina GA flowcell. T7 RNA polymerase promoter is required for transcription of the RNA of interest. The Illumina sequencing primer is used for sequencing the DNA template of the RNA of interest and serves as a docking site for the T7 RNA polymerase when it is halted. Tus protein binds to Ter site and halts the transcribing RNA polymerase. Direction of transcription and sequencing are indicated by orange and purple arrows, respectively. Tus-bound Ter site that is non-permissive (halting) and permissive (read-through) to RNA polymerase are indicated by solid and open red triangles, respectively. The halted RNA transcript includes a triplet G derived from the T7 promoter, followed by the RNA of interest and some of the Illumina sequencing primer. The 3’-end of RNA transcript, indicated by a dashed line, is inaccessible. (B) Construction of DNA templates for HiTS-RAP. DNA template is constructed by PCR in two steps using 2 sets of nested oligos. Forward oligos introduce T7 promoter (step 1) and Illumina flowcell adaptor (step 2), whereas reverse oligos introduce Illumina sequencing primer (step 1), and Ter site and Illumina flowcell adaptor 2 (step 2). (C) Sequence of the HiTS-RAP DNA template for GFP aptamer. GFP aptamer encoding sequence is in green, and the rest of the sequences are colored as in (A). The transcription start site is indicated by +1 and a broken arrow. (D) Sequence of the halted RNA transcript from GFP aptamer template. Sequences are colored as in (C). Uppercase indicates the region of the halted RNA transcript that is accessible, and the lowercase indicates a region that is likely to be buried in T7 RNA polymerase and thus inaccessible by other proteins.

    Article Snippet: 022620511 and 022620623) cBot (Illumina, cat. no. SY-301-2002) CRITICAL: For cluster generation on flowcell follow Illumina cBot™ User Guide (Part # 15006165 Rev.

    Techniques: Sequencing, Binding Assay, Derivative Assay, Construct, Polymerase Chain Reaction, Introduce