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Gaiix, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Clone Assay:

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles. ..

Amplification:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: A cDNA library suitable for sequencing on the Illumina platform was then constructed with serial amplification by PCR. .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Article Title: Astrovirus MLB2 Viremia in Febrile Child
Article Snippet: Total nucleic acid was extracted from 100 μL of the patient’s plasma by using the Roche (Indianapolis, IN, USA) MagNa Pure System and randomly amplified by using a sequence-independent PCR strategy as described ( ). .. Amplicons were sheared and, following standard library construction, were sequenced by using the Genome Analyzer IIX (Illumina Inc.) according to the manufacturer’s protocol.

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: The beads were finally resuspended in 25µl 10mM Tris pH8, of which 12.5 µl were used for the final PCR amplification (15 cycles) using specific amplification primers and Phusion DNA polymerase (Finnzymes). .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles.

Article Title: Moving pictures of the human microbiome
Article Snippet: .. Variable region 4 (V4) of 16S rRNA genes present in each community sample were amplified by PCR and subjected to multiplex sequencing on an Illumina Genome Analyzer IIx (GA-IIx; average read length after quality trimming, 123 ± 17 (standard deviation (SD)) nucleotides; 32,266 ± 19,723 (SD) reads per sample; n = 1,422 (M3 samples); n = 531 (F4 samples); average interval between sampling, 1.12 days). .. To control for differences across sequencing platforms and primer pairs, 331 of these samples had variable region 2 (V2) sequenced on 454 (average read length after quality filtering, 228 ± 11 (SD) nucleotides; 1,072 ± 375 (SD) reads per sample; n = 171 (M3 samples); n = 160 (F4 samples)).

Article Title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America
Article Snippet: Deep sequencing library generation Libraries for deep sequencing were prepared from amplified cDNA libraries using previously published protocols . .. Libraries were size-selected on a 4% polyacrylamide gel at approximately 350 bp average length, and then loaded at a final concentration of 10 pM on three lanes of a second-generation Genome Analyzer IIx (Illumina, San Diego, CA).

Autoradiography:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: A P-32 labeled 3′ RNA linker was ligated to the RNA of the IP Ago-RNA complexes “in-bead.” The Ago-RNA complexes were resolved by SDS-PAGE, transferred to nitrocellulose, and visualized by autoradiography to determine localization of the Ago-RNA complexes. .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Construct:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: A cDNA library suitable for sequencing on the Illumina platform was then constructed with serial amplification by PCR. .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: The constructs with a HindIII-specific adapter were purified using Streptavidin magnetic beads (Invitrogen) following the manufacturer's instructions. .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles.

In Silico:

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ). .. The results were compared to verify the annotation and were corrected manually by in silico molecular cloning (In Silico Biology Inc., Kanagawa, Japan).

Expressing:

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: RNA extraction, deep sequencing, RNA mapping, and expression confirmation of tRFs by northern blot. .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA).

Flow Cytometry:

Article Title: Analysis of Expressed Genes of the Bacterium 'Candidatus Phytoplasma Mali' Highlights Key Features of Virulence and Metabolism
Article Snippet: .. Barcoded libraries were sequenced on a Genome Analyzer IIx (Illumina, San Diego, California, U.S.A.) in a single read multiplex run using a half lane of the flow chamber. .. Obtained RNA-Seq reads without ambiguous read position were mapped (minimal alignment length of 90% and identity of 80%) on the genome sequence of ‘Ca .

RAST Test:

Article Title: Amoebal Endosymbiont Neochlamydia Genome Sequence Illuminates the Bacterial Role in the Defense of the Host Amoebae against Legionella pneumophila
Article Snippet: Sequencing runs for 81-mer paired-end sequence were performed using an Illumina Genome Analyzer IIx (GA IIx). .. Annotation of genes from the draft genome sequences was performed using Rapid Annotation using Subsystem Technology (RAST: http://rast.nmpdr.org/ ) with a local manual BLASTp search.

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ). .. Primary coding sequence extractions and initial function assignments were performed using the automated annotation server RAST (Rapid Annotation using Subsystem Technology) ( ).

Ligation:

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles. .. Genomic DNA was subject to complete HindIII restriction enzyme digestion and ligation to linkers.

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA). .. About 485 Mb of sequence data with a total of 32,332,590 sequence reads was generated for mock- and RSV-infected samples, using 36 b single-end sequencing reads.

Northern Blot:

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: RNA extraction, deep sequencing, RNA mapping, and expression confirmation of tRFs by northern blot. .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA).

Infection:

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: An equivalent amount of sucrose solution was added to uninfected cells, as control (mock infection). .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA).

Generated:

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

Article Title: Amoebal Endosymbiont Neochlamydia Genome Sequence Illuminates the Bacterial Role in the Defense of the Host Amoebae against Legionella pneumophila
Article Snippet: DNA clusters were generated on a slide using a Cluster Generation Kit (ver. .. Sequencing runs for 81-mer paired-end sequence were performed using an Illumina Genome Analyzer IIx (GA IIx).

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA). .. About 485 Mb of sequence data with a total of 32,332,590 sequence reads was generated for mock- and RSV-infected samples, using 36 b single-end sequencing reads.

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: This generated 976,847 reads, covering 358,569,827 bp, which were assembled into scaffolds and contigs by GS De Novo Assembler 2.6 (Newbler; Roche). .. Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ).

Polymerase Chain Reaction:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: A cDNA library suitable for sequencing on the Illumina platform was then constructed with serial amplification by PCR. .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Article Title: Astrovirus MLB2 Viremia in Febrile Child
Article Snippet: Total nucleic acid was extracted from 100 μL of the patient’s plasma by using the Roche (Indianapolis, IN, USA) MagNa Pure System and randomly amplified by using a sequence-independent PCR strategy as described ( ). .. Amplicons were sheared and, following standard library construction, were sequenced by using the Genome Analyzer IIX (Illumina Inc.) according to the manufacturer’s protocol.

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: The beads were finally resuspended in 25µl 10mM Tris pH8, of which 12.5 µl were used for the final PCR amplification (15 cycles) using specific amplification primers and Phusion DNA polymerase (Finnzymes). .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles.

Article Title: Moving pictures of the human microbiome
Article Snippet: .. Variable region 4 (V4) of 16S rRNA genes present in each community sample were amplified by PCR and subjected to multiplex sequencing on an Illumina Genome Analyzer IIx (GA-IIx; average read length after quality trimming, 123 ± 17 (standard deviation (SD)) nucleotides; 32,266 ± 19,723 (SD) reads per sample; n = 1,422 (M3 samples); n = 531 (F4 samples); average interval between sampling, 1.12 days). .. To control for differences across sequencing platforms and primer pairs, 331 of these samples had variable region 2 (V2) sequenced on 454 (average read length after quality filtering, 228 ± 11 (SD) nucleotides; 1,072 ± 375 (SD) reads per sample; n = 171 (M3 samples); n = 160 (F4 samples)).

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: Then, gap filling was performed using conventional Sanger sequencing of the PCR fragments, brute-force PCR for the contigs and scaffolds, and an ABI 3730xl DNA sequencer. .. Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ).

Article Title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America
Article Snippet: Full-length adapters were subsequently added via an additional 15 to 25 cycles of PCR. .. Libraries were size-selected on a 4% polyacrylamide gel at approximately 350 bp average length, and then loaded at a final concentration of 10 pM on three lanes of a second-generation Genome Analyzer IIx (Illumina, San Diego, CA).

Molecular Cloning:

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ). .. The results were compared to verify the annotation and were corrected manually by in silico molecular cloning (In Silico Biology Inc., Kanagawa, Japan).

RNA Sequencing Assay:

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

Article Title: Guanosine tetra- and pentaphosphate increase antibiotic tolerance by reducing reactive oxygen species production in Vibrio cholerae
Article Snippet: Paragraph title: RNA-sequencing analysis ... One lane per sample was used for sequencing with the Illumina Genome Analyzer IIx (Illumina) to generate nondirectional, single-ended, 36-base pair reads.

Article Title: Analysis of Expressed Genes of the Bacterium 'Candidatus Phytoplasma Mali' Highlights Key Features of Virulence and Metabolism
Article Snippet: Paragraph title: RNA-Seq and transcriptome analysis ... Barcoded libraries were sequenced on a Genome Analyzer IIx (Illumina, San Diego, California, U.S.A.) in a single read multiplex run using a half lane of the flow chamber.

Article Title: TNF activation of NF-κB is essential for development of single-positive thymocytes
Article Snippet: Paragraph title: RNA sequencing ... Samples were sequenced at the MRC National Institute for Medical Research High Throughput Sequencing Facility using an Illumina Genome Analyser IIx, and 36 bp single-end reads were obtained using the Illumina pipeline.

Magnetic Beads:

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: The constructs with a HindIII-specific adapter were purified using Streptavidin magnetic beads (Invitrogen) following the manufacturer's instructions. .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles.

Isolation:

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA). .. About 485 Mb of sequence data with a total of 32,332,590 sequence reads was generated for mock- and RSV-infected samples, using 36 b single-end sequencing reads.

Multiplex Assay:

Article Title: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death
Article Snippet: .. The enriched library pool was sequenced on an Illumina Genome Analyzer IIx using the manufacturer's protocols for multiplex sequencing with modifications. .. The raw reads were aligned to the PhiX 174 reference sequence to obtain a training dataset for the base caller Ibis ( ).

Article Title: Analysis of Expressed Genes of the Bacterium 'Candidatus Phytoplasma Mali' Highlights Key Features of Virulence and Metabolism
Article Snippet: .. Barcoded libraries were sequenced on a Genome Analyzer IIx (Illumina, San Diego, California, U.S.A.) in a single read multiplex run using a half lane of the flow chamber. .. Obtained RNA-Seq reads without ambiguous read position were mapped (minimal alignment length of 90% and identity of 80%) on the genome sequence of ‘Ca .

Article Title: Moving pictures of the human microbiome
Article Snippet: .. Variable region 4 (V4) of 16S rRNA genes present in each community sample were amplified by PCR and subjected to multiplex sequencing on an Illumina Genome Analyzer IIx (GA-IIx; average read length after quality trimming, 123 ± 17 (standard deviation (SD)) nucleotides; 32,266 ± 19,723 (SD) reads per sample; n = 1,422 (M3 samples); n = 531 (F4 samples); average interval between sampling, 1.12 days). .. To control for differences across sequencing platforms and primer pairs, 331 of these samples had variable region 2 (V2) sequenced on 454 (average read length after quality filtering, 228 ± 11 (SD) nucleotides; 1,072 ± 375 (SD) reads per sample; n = 171 (M3 samples); n = 160 (F4 samples)).

Labeling:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: A P-32 labeled 3′ RNA linker was ligated to the RNA of the IP Ago-RNA complexes “in-bead.” The Ago-RNA complexes were resolved by SDS-PAGE, transferred to nitrocellulose, and visualized by autoradiography to determine localization of the Ago-RNA complexes. .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Purification:

Article Title: Analysis of Expressed Genes of the Bacterium 'Candidatus Phytoplasma Mali' Highlights Key Features of Virulence and Metabolism
Article Snippet: Total RNA was purified and a DNase-digest applied using the NucleoSpin RNA II kit according to the manufacturer's instructions (Machery & Nagel, Oensingen, Switzerland). .. Barcoded libraries were sequenced on a Genome Analyzer IIx (Illumina, San Diego, California, U.S.A.) in a single read multiplex run using a half lane of the flow chamber.

Article Title: Amoebal Endosymbiont Neochlamydia Genome Sequence Illuminates the Bacterial Role in the Defense of the Host Amoebae against Legionella pneumophila
Article Snippet: Genome sequencing, annotation and prediction of metabolic pathway modules, and genome comparison Bacterial 1 kb insert DNA libraries (Purified Neochlamydia S13 and Protochlamydia R18) were prepared using a genomic DNA Sample Prep Kit (Illumina, San Diego, CA). .. Sequencing runs for 81-mer paired-end sequence were performed using an Illumina Genome Analyzer IIx (GA IIx).

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: The constructs with a HindIII-specific adapter were purified using Streptavidin magnetic beads (Invitrogen) following the manufacturer's instructions. .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles.

Sequencing:

Article Title: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death
Article Snippet: .. The enriched library pool was sequenced on an Illumina Genome Analyzer IIx using the manufacturer's protocols for multiplex sequencing with modifications. .. The raw reads were aligned to the PhiX 174 reference sequence to obtain a training dataset for the base caller Ibis ( ).

Article Title: GemSIM: general, error-model based simulator of next-generation sequencing data
Article Snippet: .. Data processing and performance We used GemSIM to calculate error models for and simulate reads from three different sequencing runs: Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry (Illumina v4); Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA (Illumina v5); and Roche/454 FLX Titanium (Roche/454). .. For the Illumina simulations, error models were calculated from PhiX control lane data aligned with Novocraft V2.07.06 [ ].

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads). ..

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

Article Title: Guanosine tetra- and pentaphosphate increase antibiotic tolerance by reducing reactive oxygen species production in Vibrio cholerae
Article Snippet: .. One lane per sample was used for sequencing with the Illumina Genome Analyzer IIx (Illumina) to generate nondirectional, single-ended, 36-base pair reads. .. Quality-filtered reads were mapped to the reference genome sequences (NCBI Bio-Project accession number PRJNA57623, identification number 57623) using CLRNASeq version 0.80 (Chunlab, Seoul, Korea).

Article Title: Analysis of Expressed Genes of the Bacterium 'Candidatus Phytoplasma Mali' Highlights Key Features of Virulence and Metabolism
Article Snippet: Single read sequencing was performed by Illumina's sequencing by synthesis approach (RNA sample preparation kit, single read cluster generation kit v4, TruSeq SBS kit v5). .. Barcoded libraries were sequenced on a Genome Analyzer IIx (Illumina, San Diego, California, U.S.A.) in a single read multiplex run using a half lane of the flow chamber.

Article Title: Astrovirus MLB2 Viremia in Febrile Child
Article Snippet: Total nucleic acid was extracted from 100 μL of the patient’s plasma by using the Roche (Indianapolis, IN, USA) MagNa Pure System and randomly amplified by using a sequence-independent PCR strategy as described ( ). .. Amplicons were sheared and, following standard library construction, were sequenced by using the Genome Analyzer IIX (Illumina Inc.) according to the manufacturer’s protocol.

Article Title: Amoebal Endosymbiont Neochlamydia Genome Sequence Illuminates the Bacterial Role in the Defense of the Host Amoebae against Legionella pneumophila
Article Snippet: .. Sequencing runs for 81-mer paired-end sequence were performed using an Illumina Genome Analyzer IIx (GA IIx). ..

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles. ..

Article Title: TNF activation of NF-κB is essential for development of single-positive thymocytes
Article Snippet: RNA-seq libraries were prepared for sequencing using Illumina Truseq RNA Library Preparation kit (Illumina) according to the manufacturer’s instructions. .. Samples were sequenced at the MRC National Institute for Medical Research High Throughput Sequencing Facility using an Illumina Genome Analyser IIx, and 36 bp single-end reads were obtained using the Illumina pipeline.

Article Title: Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift
Article Snippet: .. The DNA library was then used for cluster generation and sequencing analysis using the Genome Analyzer IIx using Illumina standard protocols. .. Methods for DNA manipulation, including sample preparation, formation of single-molecule arrays, cluster growth, and sequencing were all done by the standard protocols from Illumina, Inc. All sequencing was performed using two lanes (one for X1 and one for X2) in paired-end sequencing mode on an Illumina Genome Analyzer version 2 (GA2X) that was equipped with a 1-megapixel camera.

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA). .. About 485 Mb of sequence data with a total of 32,332,590 sequence reads was generated for mock- and RSV-infected samples, using 36 b single-end sequencing reads.

Article Title: Moving pictures of the human microbiome
Article Snippet: .. Variable region 4 (V4) of 16S rRNA genes present in each community sample were amplified by PCR and subjected to multiplex sequencing on an Illumina Genome Analyzer IIx (GA-IIx; average read length after quality trimming, 123 ± 17 (standard deviation (SD)) nucleotides; 32,266 ± 19,723 (SD) reads per sample; n = 1,422 (M3 samples); n = 531 (F4 samples); average interval between sampling, 1.12 days). .. To control for differences across sequencing platforms and primer pairs, 331 of these samples had variable region 2 (V2) sequenced on 454 (average read length after quality filtering, 228 ± 11 (SD) nucleotides; 1,072 ± 375 (SD) reads per sample; n = 171 (M3 samples); n = 160 (F4 samples)).

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: .. Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ). .. Primary coding sequence extractions and initial function assignments were performed using the automated annotation server RAST (Rapid Annotation using Subsystem Technology) ( ).

Article Title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America
Article Snippet: Paragraph title: Deep sequencing library generation ... Libraries were size-selected on a 4% polyacrylamide gel at approximately 350 bp average length, and then loaded at a final concentration of 10 pM on three lanes of a second-generation Genome Analyzer IIx (Illumina, San Diego, CA).

Immunoprecipitation:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: Cells were lysed and argonaute proteins (AGO1–4) along with the cross-linked RNA were immunoprecipitated (IP) with a murine monoclonal antibody that recognizes all human argonaute proteins (2A8 [ ], a kind gift from Dr. Zissimos Mourelatos [University of Pennsylvania, Philadelphia, PA]). .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Immunostaining:

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: Viruses in the supernatant were harvested and viral titer was determined by immunostaining in HEp-2 cells as described above. .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA).

cDNA Library Assay:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: A cDNA library suitable for sequencing on the Illumina platform was then constructed with serial amplification by PCR. .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA). .. About 485 Mb of sequence data with a total of 32,332,590 sequence reads was generated for mock- and RSV-infected samples, using 36 b single-end sequencing reads.

Agarose Gel Electrophoresis:

Article Title: Commercially Available Outbred Mice for Genome-Wide Association Studies
Article Snippet: A complementary biotinylated adapter was ligated to the sticky ends before selecting the fragments of 200 to 500 bp on a 2% agarose gel. .. The resulting libraries were verified by TOPO cloning and sequencing before running them on an Illumina Genome Analyzer IIx for 38 cycles.

Mouse Assay:

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: We recently found that strain Erdman was quite virulent compared with a clinical isolate, M. tuberculosis NCGM2209 , in BALB/c mice (strain Erdman 50% lethal dose [LD50 ], 1 × 103 /mouse; strain NCGM2209 LD50 , > 2 × 107 /mouse) (data not shown; estimated from 180-day-mortality data by the method of Reed and Muench [ ]). .. Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ).

SDS Page:

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: A P-32 labeled 3′ RNA linker was ligated to the RNA of the IP Ago-RNA complexes “in-bead.” The Ago-RNA complexes were resolved by SDS-PAGE, transferred to nitrocellulose, and visualized by autoradiography to determine localization of the Ago-RNA complexes. .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads).

Software:

Article Title: Astrovirus MLB2 Viremia in Febrile Child
Article Snippet: Amplicons were sheared and, following standard library construction, were sequenced by using the Genome Analyzer IIX (Illumina Inc.) according to the manufacturer’s protocol. .. From all reads, 238 had > 80% nt identity to the partial MLB2 sequence in GenBank (GQ502192.1) when aligned by using Cross_match software ( www.phrap.org/phredphrapconsed.html#block_phrap ).

Article Title: TNF activation of NF-κB is essential for development of single-positive thymocytes
Article Snippet: Samples were sequenced at the MRC National Institute for Medical Research High Throughput Sequencing Facility using an Illumina Genome Analyser IIx, and 36 bp single-end reads were obtained using the Illumina pipeline. .. Aligned reads were mapped to the RefSeq database and were normalized using the DESeq method ( ) using Avadis NGS software V1.3.1.

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA). .. Small RNAs were mapped using Novoalign software (Novocraft Technologies, Selangor, Malaysia) allowing two mismatches.

Article Title: Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman
Article Snippet: .. Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software ( ). .. Primary coding sequence extractions and initial function assignments were performed using the automated annotation server RAST (Rapid Annotation using Subsystem Technology) ( ).

RNA Extraction:

Article Title: Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection
Article Snippet: RNA extraction, deep sequencing, RNA mapping, and expression confirmation of tRFs by northern blot. .. The RNAs were delivered to Eureka Genomics (Houston, TX) for small RNAs isolation, directional adaptor ligation, cDNA library construction, and sequencing using a Genome Analyzer IIx (Illumina, San Diego, CA).

Selection:

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

Sample Prep:

Article Title: Guanosine tetra- and pentaphosphate increase antibiotic tolerance by reducing reactive oxygen species production in Vibrio cholerae
Article Snippet: The resulting mRNA samples were processed for the sequencing libraries using Illumina mRNA-Seq sample preparation kit (Illumina, San Diego, CA) following the manufacturer's protocols. .. One lane per sample was used for sequencing with the Illumina Genome Analyzer IIx (Illumina) to generate nondirectional, single-ended, 36-base pair reads.

Article Title: Analysis of Expressed Genes of the Bacterium 'Candidatus Phytoplasma Mali' Highlights Key Features of Virulence and Metabolism
Article Snippet: Single read sequencing was performed by Illumina's sequencing by synthesis approach (RNA sample preparation kit, single read cluster generation kit v4, TruSeq SBS kit v5). .. Barcoded libraries were sequenced on a Genome Analyzer IIx (Illumina, San Diego, California, U.S.A.) in a single read multiplex run using a half lane of the flow chamber.

Article Title: Amoebal Endosymbiont Neochlamydia Genome Sequence Illuminates the Bacterial Role in the Defense of the Host Amoebae against Legionella pneumophila
Article Snippet: Genome sequencing, annotation and prediction of metabolic pathway modules, and genome comparison Bacterial 1 kb insert DNA libraries (Purified Neochlamydia S13 and Protochlamydia R18) were prepared using a genomic DNA Sample Prep Kit (Illumina, San Diego, CA). .. Sequencing runs for 81-mer paired-end sequence were performed using an Illumina Genome Analyzer IIx (GA IIx).

Next-Generation Sequencing:

Article Title: TNF activation of NF-κB is essential for development of single-positive thymocytes
Article Snippet: .. Samples were sequenced at the MRC National Institute for Medical Research High Throughput Sequencing Facility using an Illumina Genome Analyser IIx, and 36 bp single-end reads were obtained using the Illumina pipeline. ..

Sampling:

Article Title: Moving pictures of the human microbiome
Article Snippet: .. Variable region 4 (V4) of 16S rRNA genes present in each community sample were amplified by PCR and subjected to multiplex sequencing on an Illumina Genome Analyzer IIx (GA-IIx; average read length after quality trimming, 123 ± 17 (standard deviation (SD)) nucleotides; 32,266 ± 19,723 (SD) reads per sample; n = 1,422 (M3 samples); n = 531 (F4 samples); average interval between sampling, 1.12 days). .. To control for differences across sequencing platforms and primer pairs, 331 of these samples had variable region 2 (V2) sequenced on 454 (average read length after quality filtering, 228 ± 11 (SD) nucleotides; 1,072 ± 375 (SD) reads per sample; n = 171 (M3 samples); n = 160 (F4 samples)).

Concentration Assay:

Article Title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America
Article Snippet: .. Libraries were size-selected on a 4% polyacrylamide gel at approximately 350 bp average length, and then loaded at a final concentration of 10 pM on three lanes of a second-generation Genome Analyzer IIx (Illumina, San Diego, CA). ..

Standard Deviation:

Article Title: GemSIM: general, error-model based simulator of next-generation sequencing data
Article Snippet: Data processing and performance We used GemSIM to calculate error models for and simulate reads from three different sequencing runs: Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry (Illumina v4); Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA (Illumina v5); and Roche/454 FLX Titanium (Roche/454). .. Soft-clipping was disabled, reads aligning equally well to two genomic positions were randomly aligned to one of them, and the insert size was set with a standard deviation of 200.

Article Title: Moving pictures of the human microbiome
Article Snippet: .. Variable region 4 (V4) of 16S rRNA genes present in each community sample were amplified by PCR and subjected to multiplex sequencing on an Illumina Genome Analyzer IIx (GA-IIx; average read length after quality trimming, 123 ± 17 (standard deviation (SD)) nucleotides; 32,266 ± 19,723 (SD) reads per sample; n = 1,422 (M3 samples); n = 531 (F4 samples); average interval between sampling, 1.12 days). .. To control for differences across sequencing platforms and primer pairs, 331 of these samples had variable region 2 (V2) sequenced on 454 (average read length after quality filtering, 228 ± 11 (SD) nucleotides; 1,072 ± 375 (SD) reads per sample; n = 171 (M3 samples); n = 160 (F4 samples)).

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    Illumina Inc illumina gaiix sequencer
    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, <t>Illumina</t> <t>GAIIx,</t> and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.
    Illumina Gaiix Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina gaiix sequencer/product/Illumina Inc
    Average 99 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    illumina gaiix sequencer - by Bioz Stars, 2020-02
    99/100 stars
      Buy from Supplier

    99
    Illumina Inc illumina gaiix
    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, <t>Illumina</t> <t>GAIIx,</t> and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.
    Illumina Gaiix, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 197 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina gaiix/product/Illumina Inc
    Average 99 stars, based on 197 article reviews
    Price from $9.99 to $1999.99
    illumina gaiix - by Bioz Stars, 2020-02
    99/100 stars
      Buy from Supplier

    Image Search Results


    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Journal: BMC Systems Biology

    Article Title: Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome

    doi: 10.1186/1752-0509-6-S3-S21

    Figure Lengend Snippet: The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Article Snippet: The preparing the PE library and sequencing on the Illumina GAIIx sequencer were performed according to the standard Illumina protocols (Illumina, San Diego, CA, USA).

    Techniques: Next-Generation Sequencing, Sequencing

    The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Journal: Open Biology

    Article Title: Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

    doi: 10.1098/rsob.120061

    Figure Lengend Snippet: The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Article Snippet: Each exome sample was then sequenced as paired-end reads in a full lane of an Illumina GAIIx sequencer or as a multiplexed, bar-coded sample in an Illumina HiSeq sequencer, and the resultant reads aligned to the C57BL/6 mouse reference genome using the BWA aligner [ ].

    Techniques: Sequencing, Generated, Variant Assay, Polymerase Chain Reaction

    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Journal: BMC Systems Biology

    Article Title: Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome

    doi: 10.1186/1752-0509-6-S3-S21

    Figure Lengend Snippet: The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Article Snippet: If cost allowed, the optimal outcome can be achieved with the combinations of 454 GS-FLX, Illumina GAIIx, and SOLiD4 sequencing data at abovementioned coverage depths.

    Techniques: Next-Generation Sequencing, Sequencing

    The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Journal: Open Biology

    Article Title: Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

    doi: 10.1098/rsob.120061

    Figure Lengend Snippet: The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Article Snippet: Each library sequenced on an Illumina GAIIx was sequenced on a single lane of an eight-lane flow-cell, whereas libraries sequenced on the Illumina HiSeq were multiplexed in a pool of 10 samples and sequenced together, and disambiguated using sample bar-coding.

    Techniques: Sequencing, Generated, Variant Assay, Polymerase Chain Reaction