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Illumina Inc hiseq2500
Hiseq2500, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 504 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hiseq2500/product/Illumina Inc
Average 99 stars, based on 504 article reviews
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hiseq2500 - by Bioz Stars, 2020-01
99/100 stars

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Amplification:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: Next, cDNA 3′ ends were adenylated and the adaptors were ligated followed by PCR library amplification. .. Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Article Title: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing
Article Snippet: For single cells 003G–L, 017E–I, 019B–D, 044G–H, 083G–I and 107R–U, 0.5 to 1 ng of amplified gDNA was used for library preparation using the Nextera XT kit (Illumina) following the manufacturer’s instructions. .. Samples were barcoded and multiplex sequenced, Rapid Run Mode, on a HiSeq2500 (Illumina).

Article Title: Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations
Article Snippet: Commonly, 10 purified and quantified KIR amplicon pools were combined with 10 amplicon pools targeting the HLA , blood group and CCR5 genes as described previously ( ). .. Paired-end sequencing was performed for 2 times 249 cycles with HiSeq Rapid SBS Kits v2 (500 Cycles) on HiSeq2500 (Illumina, San Diego, USA) instruments.

Article Title: Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer
Article Snippet: Equimolar concentrations of 96 libraries were pooled to a final concentration of 10 pM, denatured with 3 N NaOH, and cluster amplified with a cBot instrument on a single lane of an Illumina v3 flowcell. .. Sequencing was performed with 2 × 101 bp paired‐end reads and a 7 bp index read using SBS v3 chemistry on a HiSeq2500 (Illumina, SanDiego, CA, USA).

Article Title: Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
Article Snippet: Purified total RNA (5 ng) was amplified following the Smart-seq2 protocol . cDNA was purified using AMPure XP beads (1:1 ratio; Beckman Coulter). .. Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single-end reads.

Article Title: Exome sequencing for bipolar disorder points to roles of de novo loss-of-function and protein-altering mutations
Article Snippet: WES was performed by using either the HiSeq2000 or HiSeq2500 (Illumina, San Diego, CA, USA) with paired-end 101 bp reads. .. Identified candidates for de novo mutations were subjected to validation experiments by amplification using PCR followed by standard Sanger sequencing.

Article Title: Multiple myeloma immunoglobulin lambda translocations portend poor prognosis
Article Snippet: Size-selected libraries were purified with DNA Gel Extraction spin columns (Bio-Rad) prior to library amplification. .. Paired- end sequencing was performed using a HiSeq2000 or HiSeq2500 (Illumina) with either v3 or v4 chemistry and 86 bp reads.

Blocking Assay:

Article Title: Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma
Article Snippet: Up to 96 libraries were pooled and sequenced using 100 bp paired-end runs over 1× lane on a HiSeq2500 (Illumina). .. Hybrid capture of cfDNA libraries was performed using the Nextera Rapid Capture Exome kit (Illumina) with custom blocking oligos (IDT and Broad Institute).

Real-time Polymerase Chain Reaction:

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: Library QC: Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity > 2 nM). .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Article Title: Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations
Article Snippet: Pooled PCR products were purified with SPRIselect beads (BeckmanCoulter, Brea, USA) with a ratio of 0.6:1 beads to DNA and subsequently quantified by qPCR using the Library Quant Illumina Kit (KAPA Biosystems, Boston, USA). .. Paired-end sequencing was performed for 2 times 249 cycles with HiSeq Rapid SBS Kits v2 (500 Cycles) on HiSeq2500 (Illumina, San Diego, USA) instruments.

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: .. Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq. .. Raw sequencing reads were mapped to the human reference genome (NCBI37/hg19) using Burrows-Wheeler Aligner (BWA v0.5.8a) .

Incubation:

Article Title: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing
Article Snippet: Capture probes (4.5 μl) were added to the mixture and samples were incubated at 47 °C for 64–72 h. Post-capture, the samples were washed using Streptavidin Dynabeads (Termo Fisher Scientific, MA, USA) following the manufacturer’s protocol. .. Samples were barcoded and multiplex sequenced, Rapid Run Mode, on a HiSeq2500 (Illumina).

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: Before end-repair, a 4-hour incubation step at 65 °C was added to remove as many reversible crosslinks as possible, after which excessive single stranded DNA was removed using Mung-Bean nuclease. .. Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq.

Activity Assay:

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: Library QC: Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity > 2 nM). .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Modification:

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: The concentration of double-stranded DNA was reassessed using Pico-green and the concentration of adapters used in the ligation step of the library construction was modified based on the DNA measured. .. Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq.

Transformation Assay:

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq. .. Somatic copy number aberrations (CNAs) were identified by binning the reads in 100 Kb windows, correcting for genomic waves using the PennCNV software package and the resulting number of reads per 100 Kb window were transformed into log R-values.

Flow Cytometry:

Article Title: Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations
Article Snippet: Libraries usually consisting of 3,840 samples were loaded at 12.5 pM onto HiSeq flow cells with 10% PhiX spiked in. .. Paired-end sequencing was performed for 2 times 249 cycles with HiSeq Rapid SBS Kits v2 (500 Cycles) on HiSeq2500 (Illumina, San Diego, USA) instruments.

Ligation:

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: The concentration of double-stranded DNA was reassessed using Pico-green and the concentration of adapters used in the ligation step of the library construction was modified based on the DNA measured. .. Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq.

Nick Translation:

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H, and Escherichia coli polymerase I to generate the second strand by nick-translation. .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Generated:

Article Title: Landscape of X chromosome inactivation across human tissues
Article Snippet: Library preparation was carried out using the Nextera XT DNA Sample Kit (Illumina) with custom indexing adapters, allowing up to 384 libraries to be simultaneously generated in a 384-well PCR plate (note that DCs were processed in 384-well plate while LCL were processed in 96-well plate format). .. We sequenced one library pool per lane as paired-end 25 base reads on a HiSeq2500 (Illumina).

Article Title: CD22-CAR T Cells Induce Remissions in CD19-CAR Naïve and Resistant B-ALL
Article Snippet: .. Whole exome data was generated using Agilent SureSelectXT Human All Exon V5 and TruSeq V4 chemistry and sequenced to a median of 300× coverage using on a HiSeq2500 (Illumina). .. Whole exome and RNA-sequencing data was analyzed and mapped using the CCR Collaborative Bioinformatics Resource (CCBR) pipeline ( https://bioinformatics.cancer.gov/ ).

Article Title: Exome sequencing for bipolar disorder points to roles of de novo loss-of-function and protein-altering mutations
Article Snippet: WES was performed by using either the HiSeq2000 or HiSeq2500 (Illumina, San Diego, CA, USA) with paired-end 101 bp reads. .. Generated sequence data (fastq files) were processed by using the pipeline with BWA-MEM (version 0.7.5a), SAMtools, Picard (version 1.92, http://picard.sourceforge.net/ ) and GATK (version 2.6–4).

Article Title: CD22-CAR T Cells Induce Remissions in CD19-CAR Naïve and Resistant B-ALL
Article Snippet: .. Poly-adenylated RNA libraries were generated and sequenced using TruSeq 4.0 chemistry on a Hiseq2500 (Illumina). .. Whole exome data was generated using Agilent SureSelectXT Human All Exon V5 and TruSeq V4 chemistry and sequenced to a median of 300× coverage using on a HiSeq2500 (Illumina).

Sequencing:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads. .. Sequencing reads were pre-processed with a pipeline that included FastQC and Cutadapt filtering and trimming.

Article Title: Multiple ABCB1 transcriptional fusions in drug resistant high-grade serous ovarian and breast cancer
Article Snippet: Paragraph title: Transcriptome sequencing ... All libraries were sequenced as paired-end 100 bp on a HiSeq2500 (Illumina, at AGRF), generating 100 million paired reads per sample.

Article Title: MMP21 is mutated in human heterotaxy and is required for normal left-right asymmetry in vertebrates
Article Snippet: .. Paired-end sequencing (75 bp + 75 bp reads) was carried out on a pool of barcoded exome librairies using a HiSeq2500 (Illumina). ..

Article Title: Landscape of X chromosome inactivation across human tissues
Article Snippet: Paragraph title: Single cell data preparation and sequencing ... We sequenced one library pool per lane as paired-end 25 base reads on a HiSeq2500 (Illumina).

Article Title: Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma
Article Snippet: Paragraph title: cfDNA sequencing ... Up to 96 libraries were pooled and sequenced using 100 bp paired-end runs over 1× lane on a HiSeq2500 (Illumina).

Article Title: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing
Article Snippet: Paragraph title: Library preparation and sequencing of DTCs and primary tumors with matched blood ... Samples were barcoded and multiplex sequenced, Rapid Run Mode, on a HiSeq2500 (Illumina).

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina). ..

Article Title: Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations
Article Snippet: .. Paired-end sequencing was performed for 2 times 249 cycles with HiSeq Rapid SBS Kits v2 (500 Cycles) on HiSeq2500 (Illumina, San Diego, USA) instruments. .. Nextype for KIR The general design of the neXtype software for KIR allele-level genotyping follows the design of neXtype for HLA genotyping as described previously ( ).

Article Title: Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer
Article Snippet: .. Sequencing was performed with 2 × 101 bp paired‐end reads and a 7 bp index read using SBS v3 chemistry on a HiSeq2500 (Illumina, SanDiego, CA, USA). .. We used our targeted tumour sequencing bioinformatics pipeline for data analysis .

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: Paragraph title: Low-coverage whole genome sequencing ... Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq.

Article Title: Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
Article Snippet: From this step, 1 ng cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA library preparation kit (catalog# FC-131-1096) and index kit (set B and C, catalog# FC-131-2002 and FC-131-2003, respectively), Illumina). .. Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single-end reads.

Article Title: Exome sequencing for bipolar disorder points to roles of de novo loss-of-function and protein-altering mutations
Article Snippet: Paragraph title: Exome sequencing, data processing, variant calling and identification of de novo mutations ... WES was performed by using either the HiSeq2000 or HiSeq2500 (Illumina, San Diego, CA, USA) with paired-end 101 bp reads.

Article Title: Multiple myeloma immunoglobulin lambda translocations portend poor prognosis
Article Snippet: .. Paired- end sequencing was performed using a HiSeq2000 or HiSeq2500 (Illumina) with either v3 or v4 chemistry and 86 bp reads. .. Raw sequencing data was extracted from BCL files using BCL2FASTQ v2.17.1 to extract FASTQ files.

RNA Sequencing Assay:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: Paragraph title: RNA sequencing ... Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Article Title: Multiple ABCB1 transcriptional fusions in drug resistant high-grade serous ovarian and breast cancer
Article Snippet: All libraries were sequenced as paired-end 100 bp on a HiSeq2500 (Illumina, at AGRF), generating 100 million paired reads per sample. .. RNA-seQC was used to investigate RNA sequencing quality.

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: Sequencing: Libraries were sequenced on HiSeq2500 (Illumina). .. RNA-seq Adapter sequences (Oligonucleotide sequences of adapters from TruSeqTM RNA and DNA Sample Prep Kits): RNA 5ʹ Adapter (RA5), part # 15013205: 5ʹ-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3ʹ RNA 3ʹ Adapter (RA3), part # 15013207: 5ʹ-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (6-nucleotide index) ATCTCGTATGCCGTCTTCTGCTTG-3ʹ Mapping to a reference genome: Algorithm for mapping sequences: appropriate software was chosen according to the characteristics of the reference genome.

Article Title: CD22-CAR T Cells Induce Remissions in CD19-CAR Naïve and Resistant B-ALL
Article Snippet: Whole exome data was generated using Agilent SureSelectXT Human All Exon V5 and TruSeq V4 chemistry and sequenced to a median of 300× coverage using on a HiSeq2500 (Illumina). .. Whole exome and RNA-sequencing data was analyzed and mapped using the CCR Collaborative Bioinformatics Resource (CCBR) pipeline ( https://bioinformatics.cancer.gov/ ).

Article Title: Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
Article Snippet: Paragraph title: RNA sequencing ... Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single-end reads.

Magnetic Beads:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: In brief, poly A+ RNA was purified using poly-T oligo-attached magnetic beads with two rounds of purification followed by fragmentation and first and second cDNA strand synthesis. .. Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Isolation:

Article Title: CD22-CAR T Cells Induce Remissions in CD19-CAR Naïve and Resistant B-ALL
Article Snippet: Leukemia samples from bone marrow specimens containing greater than 90% leukemia were isolated by density gradient separation using Lymphocyte Separation Medium (Lonzo). .. Whole exome data was generated using Agilent SureSelectXT Human All Exon V5 and TruSeq V4 chemistry and sequenced to a median of 300× coverage using on a HiSeq2500 (Illumina).

Purification:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: In brief, poly A+ RNA was purified using poly-T oligo-attached magnetic beads with two rounds of purification followed by fragmentation and first and second cDNA strand synthesis. .. Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Article Title: Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations
Article Snippet: Commonly, 10 purified and quantified KIR amplicon pools were combined with 10 amplicon pools targeting the HLA , blood group and CCR5 genes as described previously ( ). .. Paired-end sequencing was performed for 2 times 249 cycles with HiSeq Rapid SBS Kits v2 (500 Cycles) on HiSeq2500 (Illumina, San Diego, USA) instruments.

Article Title: Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
Article Snippet: Purified total RNA (5 ng) was amplified following the Smart-seq2 protocol . cDNA was purified using AMPure XP beads (1:1 ratio; Beckman Coulter). .. Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single-end reads.

Article Title: Multiple myeloma immunoglobulin lambda translocations portend poor prognosis
Article Snippet: Size-selected libraries were purified with DNA Gel Extraction spin columns (Bio-Rad) prior to library amplification. .. Paired- end sequencing was performed using a HiSeq2000 or HiSeq2500 (Illumina) with either v3 or v4 chemistry and 86 bp reads.

Polymerase Chain Reaction:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: Next, cDNA 3′ ends were adenylated and the adaptors were ligated followed by PCR library amplification. .. Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Article Title: Landscape of X chromosome inactivation across human tissues
Article Snippet: Library preparation was carried out using the Nextera XT DNA Sample Kit (Illumina) with custom indexing adapters, allowing up to 384 libraries to be simultaneously generated in a 384-well PCR plate (note that DCs were processed in 384-well plate while LCL were processed in 96-well plate format). .. We sequenced one library pool per lane as paired-end 25 base reads on a HiSeq2500 (Illumina).

Article Title: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing
Article Snippet: Subsequently, post-capture PCR was performed for ten cycles. .. Samples were barcoded and multiplex sequenced, Rapid Run Mode, on a HiSeq2500 (Illumina).

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Article Title: Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations
Article Snippet: Pooled PCR products were purified with SPRIselect beads (BeckmanCoulter, Brea, USA) with a ratio of 0.6:1 beads to DNA and subsequently quantified by qPCR using the Library Quant Illumina Kit (KAPA Biosystems, Boston, USA). .. Paired-end sequencing was performed for 2 times 249 cycles with HiSeq Rapid SBS Kits v2 (500 Cycles) on HiSeq2500 (Illumina, San Diego, USA) instruments.

Article Title: Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer
Article Snippet: Following capture, each library was PCR amplified for 13 cycles with primers containing a unique 6 bp index. .. Sequencing was performed with 2 × 101 bp paired‐end reads and a 7 bp index read using SBS v3 chemistry on a HiSeq2500 (Illumina, SanDiego, CA, USA).

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: For the library enrichment, 5–15 cycles of PCR with intermediate assessment steps were used instead to ensure low adapter dimer content and high library yield. .. Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq.

Article Title: Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
Article Snippet: Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single-end reads. .. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection (Bioanalyzer, Agilent).

Article Title: Exome sequencing for bipolar disorder points to roles of de novo loss-of-function and protein-altering mutations
Article Snippet: WES was performed by using either the HiSeq2000 or HiSeq2500 (Illumina, San Diego, CA, USA) with paired-end 101 bp reads. .. Identified candidates for de novo mutations were subjected to validation experiments by amplification using PCR followed by standard Sanger sequencing.

cDNA Library Assay:

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Sample Prep:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: For RNA-seq library preparation, 500 ng of total RNA were processed using the TruSeq RNA sample preparation kit v2 (Illumina RS-122-2001) following manufacturer’s instructions. .. Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Article Title: Multiple ABCB1 transcriptional fusions in drug resistant high-grade serous ovarian and breast cancer
Article Snippet: Transcriptome sequencing One microgram of total RNA was used for library preparation using the TruSeq RNA Sample Preparation kit (Illumina) as per the manufacturer’s low-throughput protocol. .. All libraries were sequenced as paired-end 100 bp on a HiSeq2500 (Illumina, at AGRF), generating 100 million paired reads per sample.

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: Sequencing: Libraries were sequenced on HiSeq2500 (Illumina). .. RNA-seq Adapter sequences (Oligonucleotide sequences of adapters from TruSeqTM RNA and DNA Sample Prep Kits): RNA 5ʹ Adapter (RA5), part # 15013205: 5ʹ-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3ʹ RNA 3ʹ Adapter (RA3), part # 15013207: 5ʹ-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (6-nucleotide index) ATCTCGTATGCCGTCTTCTGCTTG-3ʹ Mapping to a reference genome: Algorithm for mapping sequences: appropriate software was chosen according to the characteristics of the reference genome.

Article Title: Multiple myeloma immunoglobulin lambda translocations portend poor prognosis
Article Snippet: Libraries were prepared with either the TruSeq DNA Sample Prep (Illumina) or Hyper Prep (Kapa Biosystems) following the manufacturer’s instructions using AMPure beads (Invitrogen) for clean-up. .. Paired- end sequencing was performed using a HiSeq2000 or HiSeq2500 (Illumina) with either v3 or v4 chemistry and 86 bp reads.

Chromatin Immunoprecipitation:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit fluorometer (Life Technologies). .. Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Article Title: Landscape of X chromosome inactivation across human tissues
Article Snippet: The concentration of the final pooled libraries was measured using the High-Sensitivity DNA Qubit (Life Technologies), and the size distribution measured on a High-Sensitivity Bioanalyzer Chip (Agilent). .. We sequenced one library pool per lane as paired-end 25 base reads on a HiSeq2500 (Illumina).

Software:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads. .. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: Sequencing: Libraries were sequenced on HiSeq2500 (Illumina). .. RNA-seq Adapter sequences (Oligonucleotide sequences of adapters from TruSeqTM RNA and DNA Sample Prep Kits): RNA 5ʹ Adapter (RA5), part # 15013205: 5ʹ-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3ʹ RNA 3ʹ Adapter (RA3), part # 15013207: 5ʹ-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (6-nucleotide index) ATCTCGTATGCCGTCTTCTGCTTG-3ʹ Mapping to a reference genome: Algorithm for mapping sequences: appropriate software was chosen according to the characteristics of the reference genome.

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq. .. Somatic copy number aberrations (CNAs) were identified by binning the reads in 100 Kb windows, correcting for genomic waves using the PennCNV software package and the resulting number of reads per 100 Kb window were transformed into log R-values.

Multiplex Assay:

Article Title: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing
Article Snippet: .. Samples were barcoded and multiplex sequenced, Rapid Run Mode, on a HiSeq2500 (Illumina). .. Copy number analysis of primary tumors DNA from the primary tumors or lymph node metastasis was analyzed for CNAs using the Genome-Wide Human SNP array 6.0 platform (Affymetrix, Santa Clara, CA, USA).

Selection:

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Article Title: Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
Article Snippet: Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single-end reads. .. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection (Bioanalyzer, Agilent).

Agarose Gel Electrophoresis:

Article Title: Multiple myeloma immunoglobulin lambda translocations portend poor prognosis
Article Snippet: Adapter ligated libraries were run on a 1.5% agarose gel and extracted by hand or with an Extracta-gel-extractor (USA Scientific). .. Paired- end sequencing was performed using a HiSeq2000 or HiSeq2500 (Illumina) with either v3 or v4 chemistry and 86 bp reads.

Concentration Assay:

Article Title: CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation
Article Snippet: Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit fluorometer (Life Technologies). .. Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 × single reads.

Article Title: Landscape of X chromosome inactivation across human tissues
Article Snippet: Expected concentration of the pooled libraries was 10-30 ng/μL with size distribution of 300-700bp. .. We sequenced one library pool per lane as paired-end 25 base reads on a HiSeq2500 (Illumina).

Article Title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Article Snippet: Library QC: Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity > 2 nM). .. Sequencing: Libraries were sequenced on HiSeq2500 (Illumina).

Article Title: Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer
Article Snippet: Equimolar concentrations of 96 libraries were pooled to a final concentration of 10 pM, denatured with 3 N NaOH, and cluster amplified with a cBot instrument on a single lane of an Illumina v3 flowcell. .. Sequencing was performed with 2 × 101 bp paired‐end reads and a 7 bp index read using SBS v3 chemistry on a HiSeq2500 (Illumina, SanDiego, CA, USA).

Article Title: Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy
Article Snippet: The concentration of double-stranded DNA was reassessed using Pico-green and the concentration of adapters used in the ligation step of the library construction was modified based on the DNA measured. .. Following quantification with qPCR, the resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage (±0.1×) for shallow-seq.

Gel Extraction:

Article Title: Multiple myeloma immunoglobulin lambda translocations portend poor prognosis
Article Snippet: Size-selected libraries were purified with DNA Gel Extraction spin columns (Bio-Rad) prior to library amplification. .. Paired- end sequencing was performed using a HiSeq2000 or HiSeq2500 (Illumina) with either v3 or v4 chemistry and 86 bp reads.

Variant Assay:

Article Title: MMP21 is mutated in human heterotaxy and is required for normal left-right asymmetry in vertebrates
Article Snippet: Paired-end sequencing (75 bp + 75 bp reads) was carried out on a pool of barcoded exome librairies using a HiSeq2500 (Illumina). .. Downstream processing was performed using Genome Analysis Toolkit (GATK), SAMtools and Picard, and variant calls were made with the GATK Unified Genotyper.

Article Title: CD22-CAR T Cells Induce Remissions in CD19-CAR Naïve and Resistant B-ALL
Article Snippet: Whole exome data was generated using Agilent SureSelectXT Human All Exon V5 and TruSeq V4 chemistry and sequenced to a median of 300× coverage using on a HiSeq2500 (Illumina). .. Somatic variant calling was performed using MuTect and copy number alterations were analyzed using Nexus Copy Number Discovery Edition #9. (BioDiscovery).

Article Title: Exome sequencing for bipolar disorder points to roles of de novo loss-of-function and protein-altering mutations
Article Snippet: Paragraph title: Exome sequencing, data processing, variant calling and identification of de novo mutations ... WES was performed by using either the HiSeq2000 or HiSeq2500 (Illumina, San Diego, CA, USA) with paired-end 101 bp reads.

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    Illumina Inc nextera rapid capture exome kit
    Nextera Rapid Capture Exome Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 92 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextera rapid capture exome kit/product/Illumina Inc
    Average 90 stars, based on 92 article reviews
    Price from $9.99 to $1999.99
    nextera rapid capture exome kit - by Bioz Stars, 2020-01
    90/100 stars
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    90
    Illumina Inc hiseq sbs kit
    Hiseq Sbs Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq sbs kit/product/Illumina Inc
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hiseq sbs kit - by Bioz Stars, 2020-01
    90/100 stars
      Buy from Supplier

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