Library pools were clustered onto Illumina v3 flowcells using the Illumina Truseq PE Cluster Kit v3 on the Illumina cBot. Clustered flowcells were sequenced by synthesis on the Illumina HiSeq2000 using Illumina’s Truseq PE Cluster Kit v3 and Illumina’s TruSeq SBS Kits v3 for paired 83 base pair read lengths.
Truseq pe cluster kit v3
Manufactured by Illumina
Sourced in United States
The TruSeq PE Cluster Kit v3 is a laboratory equipment product manufactured by Illumina. It is designed to prepare DNA samples for sequencing on Illumina's sequencing platforms. The kit includes reagents and consumables necessary for cluster generation, which is the process of creating dense clusters of clonal DNA fragments on a flow cell. This is a crucial step in Illumina's sequencing workflow, enabling the subsequent identification and analysis of the genetic sequences.
Automatically generated - may contain errors
Lab products found in correlation
Truseq sbs kit v3, by Illumina (29 mentions)
Hiseq 2000, by Illumina (18 mentions)
Cbot workstation, by Illumina (10 mentions)
Hiseq 1000, by Illumina (7 mentions)
Hiseq 2500, by Illumina (5 mentions)
Hiseq 1500, by Illumina (5 mentions)
Fragmentation buffer, by Illumina (5 mentions)
Truseq rna sample preparation kit, by Illumina (5 mentions)
Truseq rna sample prep kit, by Illumina (5 mentions)
Hiseq 2000 platform, by Illumina (5 mentions)
Truseq sbs kit v3 hs, by Illumina (5 mentions)
Truseq rna sample preparation kit v2, by Illumina (5 mentions)
Hiseq 2000 sequencer, by Illumina (4 mentions)
Truseq sbs v3 chemistry, by Illumina (3 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions)
Hiseq 2500 sequencer, by Illumina (3 mentions)
Qpcr library quantification kit, by Agilent Technologies (3 mentions)
Tapestation 2200, by Agilent Technologies (3 mentions)
Casava 1, by Illumina (3 mentions)
Truseq dna sample prep kit, by Illumina (3 mentions)
64 protocols using truseq pe cluster kit v3
1
Illumina Paired-End Sequencing Procedure
2
Illumina HiSeq Paired-End Sequencing
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Denatured and diluted libraries with a 1% phiX spike-in were used to generate clusters on Illumina's HiSeq Paired End v3 flowcell on the Illumina cBot using Illumina's TruSeq PE Cluster Kit v3 (catalog #PE-401-3001). The clustered flowcell was sequenced by synthesis on the Illumina HiSeq 2000 for paired 100-bp reads using Illumina's TruSeq SBS Kit V3 (catalog #FC-401-3001).
3
Genome sequencing of Streptococcus tigurinus strains
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Genomic DNA from S. tigurinus strains AZ_8, AZ_14, ATCC15914 and 859 were purified using a Wizard Genomic DNA purification kit (Promega, Dübendorf, Switzerland). Genomic DNA libraries from AZ_8, AZ_14, and 859 were prepared using 1μg of the purified genomic DNA and the TruSeq DNA LT Sample Preparation Kit according to the manufacturer’s protocol (Illumina, San Diego, USA; Cat. No. FC-121-2001). The resulting libraries were pooled into a single library for paired-end sequencing of 2x100-bp on the Illumina HiSeq 2500 using TruSeq PE Cluster Kit v3 (Cat. No. PE-401-3001) and TruSeq SBS Kit v3 (Cat. No. FC-401-3001). Data were processed using the Illumina Pipeline Software package v1.82 and aligned using Eland v2e. Assembly of paired-end reads was done with Edena [13 (link)]. ATCC15914 isolate was sequenced using the PacBio (Pacific Biosciences) technology [14 (link)]. Contigs were submitted to NCBI for automated annotation and publication in databases. Assembled contigs of strains AZ_3aT, 1366, 2425, 2426 or full genome of Streptococcus oralis strain Uo5 (closest relative of S. tigurinus) and full annotations were obtained from NCBI (accession numbers: AORU01, AORX01, ASWZ01, ASXA01, 331265438 respectively). Full genome of Streptococcus oralis strain Uo5, which is the closest relative of S. tigurinus, was obtained from NCBI (accession number 331265438).
4
Small RNA Profiling of SW480/SW620 Cells and EVs
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Small RNA (18~30 nt) libraries for SW480/SW620 cells and derived EVs (sMVs and exosomes) were constructed using Illumina TruSeq Small RNA Sample Preparation Kit v2 and sequenced on a HiSeq 2000 platform (Illumina), according to the manufacturer’s protocols. Briefly, small RNAs (18~30 nt) were fractioned on a 15% Tris-borate-EDTA (TBE) polyacrylamide gel (Life Technologies, CA) from total RNA (200 ng), purified by centrifugation, and ligated with adaptors. Small RNAs were then reverse transcribed into cDNAs and amplified using the adaptor primers for 14 cycles. The cDNA fragments (~150 bp) were isolated from a 6% TBE PAGE-gel and directly used for cluster generation by using TruSeq PE Cluster Kit v3 (Illumina). Using TruSeq SBS Kit v3 (Illumina) biological replicates (n = 2) were sequenced for each sample.
5
Sequence-Independent Single Primer Amplification for Viral Discovery
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Sequences were assembled using sequence-independent single primer amplification (SISPA) to barcode random primed cDNAs [29 (link), 30 (link)] from individual cDNA samples. SISPA products were normalized and pooled into a single reaction that was purified using a PCR purification kit (Qiagen, Valencia, CA). Samples were subsequently gel purified to select for products ranging from 300-500bp in size for sequencing with the Illumina Genome Analyzer II or 500-800bp in size for Roche 454 Titanium (GS-FLX) sequencing [31 (link)], or were sequenced on the Illumina HiSeq using the following protocol; cDNA (0.05–1.7 μg) was fragmented by incubation at 94°C for eight (8) minutes in 19.5 ul of fragmentation buffer (Illumina 15016648). Samples were tracked using the “index tags” incorporated into the adapters as defined by the manufacturer. Cluster formation of the library DNA templates was performed using the TruSeq PE Cluster Kit v3 (Illumina) and the Illumina cBot workstation using conditions recommended by the manufacturer. Paired end 50 base sequencing by synthesis was performed using TruSeq SBS kit v3 (Illumina) on an Illumina HiSeq 1500 using protocols defined by the manufacturer.
6
Transcriptome Sequencing Using Illumina HiSeq
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Each transcriptome was loaded to occupy one third of the lane capacity in the flow cell. The cBot-2 system and TruSeq PE Cluster Kit v3 (Illumina, San Diego, CA, USA) were used for cluster generation, and TruSeq SBS Kit v3-HS reagent kit and HiSeq2000 instrument (Illumina, San Diego, CA, USA) was used to generate paired 100-bp reads according to the manufacturer’s instructions. Nextera Read Primers 1 and 2 as well as Nextera Index Read Primer (Illumina) were used for paired-end sequencing and index read sequencing, respectively.
7
Whole Genome Sequencing and Copy Number Analysis
8
RNA-seq analysis of human islet cells
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Thawed islets (n = 32 donors) or freshly isolated islets (n = 18 donors) were hand-picked and RNA was extracted using Trizol reagent (Life Technologies). RNA sequencing was performed on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) with 100 bp paired-end sequencing. Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, Hitchin, UK) with custom 8 bp indexes [29 (link)]. The TruSeq PE Cluster Kit v3 (Illumina) was used for cluster generation and the TruSeq SBS Kit v3 (Illumina) for sequencing. Sequenced reads were mapped to the human genome (GRCh37) with Tophat v2.0.12 (www.ccb.jhu.edu/software/tophat/index.shtml ) [30 (link)] using Gencode v18 (www.gencodegenes.org ) as the transcriptome reference. Expression was quantified using Cuffquant and Cuffnorm (http://cole-trapnell-lab.github.io/cufflinks/ ) [30 (link)] on default settings.
9
RNA, ChIP, and Single-cell RNA Sequencing Protocols
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Library preparation for RNA sequencing (RNA-seq) was performed as described76 (link) using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and 100–110 ng of total RNA. Library preparation for ChIP-sequencing (ChIP-seq) was performed as previously described77 (link) using the KAPA LTP Library Preparation Kit (KAPA Biosystems) and 2 ng of input DNA, or the entire amount of the ChIP DNA obtained. The KAPA Real-Time Library Amplification Kit (KAPA Biosystems) was used in conjunction with the library preparation kits (TruSeq Stranded mRNA Library Prep Kit) to minimize the number of PCR cycles for library amplification. Library preparation for single-cell RNA-seq (scRNA-seq) was performed following the standard protocol of the 10x Genomics Chromium Single Cell 3′ v2 Kit (10x Genomics). Sequencing was performed in HiSeq1500 (Illumina) with the HiSeq SR Rapid Cluster Kit v2 (Illumina), the HiSeq PE Rapid Cluster Kit v2 (Illumina), or the TruSeq PE Cluster Kit v3-cBot-HS, to obtain single-end 80 nt reads for RNA-seq and ChIP-seq libraries, or paired-end 26 nt (Read 1)- 98 nt (Read 2) reads for scRNA-seq libraries. The total reads of each sample are listed in Supplementary Data 7 .
10
RNA-Seq Library Preparation and Sequencing
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Poly-A+ RNA was selected from total RNA (1 μg) using oligo dT-attached magnetic beads. Bound RNA was fragmented by incubation at 94 °C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina). First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit under conditions prescribed by the manufacturer (Illumina). Samples were tracked using “index tags” incorporated into the adapters. Library quality was evaluated using an Agilent DNA-1000 chip on an Agilent 2100 Bioanalyzer. Quantification of library DNA templates was performed using qPCR and a known-size reference standard. Cluster formation of the library DNA templates was performed using the TruSeq PE Cluster Kit v3 (Illumina) and the Illumina cBot workstation using conditions recommended by the manufacturer. Template input was adjusted to obtain a cluster density of 700–900 K/mm2. Paired end 50 base sequencing by synthesis was performed using TruSeq SBS kit v3 (Illumina) on an Illumina HiSeq 1000 using protocols defined by the manufacturer.
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