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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 351 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/illumina cbot/product/Illumina Inc
Average 99 stars, based on 351 article reviews
Price from $9.99 to $1999.99
illumina cbot - by Bioz Stars, 2020-09
99/100 stars

Images

1) Product Images from "Lane-by-lane sequencing using Illumina’s Genome Analyzer II"

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

Journal: BioTechniques

doi: 10.2144/000114032

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.
Figure Legend 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.

Techniques Used: Sequencing, Flow Cytometry

2) Product Images from "Lane-by-lane sequencing using Illumina’s Genome Analyzer II"

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

Journal: BioTechniques

doi: 10.2144/000114032

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.
Figure Legend 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.

Techniques Used: Sequencing, Flow Cytometry

Related Articles

Flow Cytometry:

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: .. Each pool was normalized to 10 pM, loaded and clustered to individual lanes of a HiSeq Flow Cell using an Illumina cBot (TruSeq PE Cluster Kit v3), followed by 2 × 101 PE sequencing on a HiSeq2000 sequencer according to the manufacturer's recommended protocol (Illumina Inc.). .. Detection of somatic sequence mutations in primary tumor High quality paired-end reads passing Illumina RTA filter were aligned to the NCBI human reference genome (GRCh37) using BWA [ ].

Amplification:

Article Title: Transcriptome analysis unravels spatiotemporal modulation of phytohormone-pathway expression underlying gibberellin-induced parthenocarpic fruit set in San Pedro-type fig (Ficus carica L.)
Article Snippet: .. After bridge PCR amplification on Illumina cBot using Truseq PE Cluster Kit v3-cBot-HS, paired-end (2 × 151 bp) sequencing of the cDNA library products was carried out using the Illumina HiSeq4000 platform. .. Illumina read processing and functional annotation Clean reads were generated by removing reads with adaptors and more than 10% unknown nucleotides, and low-quality reads (the rate of reads with quality value ≤10 was more than 20%) from the raw data.

Generated:

Article Title: Studies on Colony Stimulating Factor Receptor-1 and Ligands Colony Stimulating Factor-1 and Interleukin-34 in Alzheimer's Disease Brains and Human Microglia
Article Snippet: .. Clusters were generated on Paired End v3 flowcells in the Illumina cBot using Illumina's TruSeq PE Cluster Kit v3, which were sequenced by synthesis on the Illumina HiSeq 2000 for paired 100-bp reads. .. Due to the small number of samples, data analysis was restricted to estimation of FPKM (fragments per kilobase of exon per million fragments mapped), a digital count of each transcript adjusted for its overall size using TopHat/Cufflinks/Cuffdiff software.

Sequencing:

Article Title: Transcriptome analysis unravels spatiotemporal modulation of phytohormone-pathway expression underlying gibberellin-induced parthenocarpic fruit set in San Pedro-type fig (Ficus carica L.)
Article Snippet: .. After bridge PCR amplification on Illumina cBot using Truseq PE Cluster Kit v3-cBot-HS, paired-end (2 × 151 bp) sequencing of the cDNA library products was carried out using the Illumina HiSeq4000 platform. .. Illumina read processing and functional annotation Clean reads were generated by removing reads with adaptors and more than 10% unknown nucleotides, and low-quality reads (the rate of reads with quality value ≤10 was more than 20%) from the raw data.

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: .. Each pool was normalized to 10 pM, loaded and clustered to individual lanes of a HiSeq Flow Cell using an Illumina cBot (TruSeq PE Cluster Kit v3), followed by 2 × 101 PE sequencing on a HiSeq2000 sequencer according to the manufacturer's recommended protocol (Illumina Inc.). .. Detection of somatic sequence mutations in primary tumor High quality paired-end reads passing Illumina RTA filter were aligned to the NCBI human reference genome (GRCh37) using BWA [ ].

Article Title: Enforcement of developmental lineage specificity by transcription factor Oct1
Article Snippet: .. Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot. .. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot.

Article Title: Evolution of Vertebrate Phototransduction: Cascade Activation
Article Snippet: .. Clustering and Sequencing (E. cirrhatus and G. australis, February 2013) For this first set, clustering was performed on an Illumina cBot using the Illumina TruSeq PE Cluster kit v3—HS (catalog # PE-401-3001) according to the cBot User Guide (part #15006165). ..

Bridge PCR:

Article Title: Transcriptome analysis unravels spatiotemporal modulation of phytohormone-pathway expression underlying gibberellin-induced parthenocarpic fruit set in San Pedro-type fig (Ficus carica L.)
Article Snippet: .. After bridge PCR amplification on Illumina cBot using Truseq PE Cluster Kit v3-cBot-HS, paired-end (2 × 151 bp) sequencing of the cDNA library products was carried out using the Illumina HiSeq4000 platform. .. Illumina read processing and functional annotation Clean reads were generated by removing reads with adaptors and more than 10% unknown nucleotides, and low-quality reads (the rate of reads with quality value ≤10 was more than 20%) from the raw data.

cDNA Library Assay:

Article Title: Transcriptome analysis unravels spatiotemporal modulation of phytohormone-pathway expression underlying gibberellin-induced parthenocarpic fruit set in San Pedro-type fig (Ficus carica L.)
Article Snippet: .. After bridge PCR amplification on Illumina cBot using Truseq PE Cluster Kit v3-cBot-HS, paired-end (2 × 151 bp) sequencing of the cDNA library products was carried out using the Illumina HiSeq4000 platform. .. Illumina read processing and functional annotation Clean reads were generated by removing reads with adaptors and more than 10% unknown nucleotides, and low-quality reads (the rate of reads with quality value ≤10 was more than 20%) from the raw data.

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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 396 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina cbot/product/Illumina Inc
    Average 99 stars, based on 396 article reviews
    Price from $9.99 to $1999.99
    illumina cbot - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    88
    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: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/flowcell follow illumina cbot user guide/product/Illumina Inc
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    flowcell follow illumina cbot user guide - by Bioz Stars, 2020-09
    88/100 stars
      Buy from Supplier

    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