Vero cells in T25 flasks were infected with each mutant strain. At time of harvest, EBs were concentrated from cell lysates by centrifugation (21,000 × g, 15 minutes, 4 °C), and resuspended in DNAse I reaction buffer (NEB Labs). Residual host DNA was digested with 8 Units of DNAse I (NEB) for 1 hour at 37 °C and EBs washed with PBS, pelleted, and resuspended in 180 μl of ATL buffer (Qiagen). Total DNA was isolated with a Qiagen DNeasy Blood and Tissue Kit (Qiagen). 150 ng of total DNA isolated from each of 20 individual strains were pooled with 150 ng of control DNA. One μg of pooled DNA was sheared with an Adaptive Focused Acoustics S220 instrument (Covaris). Sequencing libraries were prepared and barcoded with a TrueSeq DNA sample preparation kit (Illumina Inc.) and sequenced on a HiSeq2000 sequencing platform (Illumina Inc.).
Trueseq dna sample preparation kit
Manufactured by Illumina
Sourced in United States
The TruSeq DNA Sample Preparation Kit is a laboratory equipment product from Illumina. The kit provides reagents and protocols for preparing DNA samples for sequencing on Illumina sequencing platforms. The core function of the kit is to enable the processing of DNA samples to generate libraries suitable for analysis on Illumina sequencing instruments.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq 1000, by Illumina (2 mentions)
Miseq platform, by Illumina (2 mentions)
2100 bioanalyzer, by Agilent Technologies (2 mentions)
Atl buffer, by Qiagen (1 mentions)
Dnase 1, by New England Biolabs (1 mentions)
Dneasy blood and tissue kit, by Qiagen (1 mentions)
Hiseq 2000 sequencing platform, by Illumina (1 mentions)
S220 instrument, by Covaris (1 mentions)
Ampure xp reagent, by Beckman Coulter (1 mentions)
Trueseq sbs kit v3, by Illumina (1 mentions)
Abi 7900ht system, by Thermo Fisher Scientific (1 mentions)
Trueseq dna sample prep kit, by Illumina (1 mentions)
Kapa library quant kit, by Roche (1 mentions)
Hiseq 2000 system, by Illumina (1 mentions)
Rapid library preparation kit, by Roche (1 mentions)
Truseq rna library prep kit v2, by Illumina (1 mentions)
Hiseq 2500, by Illumina (1 mentions)
Sequencing platform, by Illumina (1 mentions)
Sureselect human all exome kit, by Agilent Technologies (1 mentions)
Hiseq 1000 instrument, by Illumina (1 mentions)
10 protocols using trueseq dna sample preparation kit
1
Chlamydia Genomic DNA Extraction
2
Whole Genome Sequencing Library Preparation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
TrueSeq DNA Sample Preparation Kit (Illumina) was used to prepare the WGS library from purified genomic DNA sample of Comp1 strain. The quality and concentration of isolated DNA was assessed for OD260/OD280 ratio > 1.8, OD260/OD230 ratio > 1.9, DNA concentration between 250 to 500 ng/μl and no visible evidence of DNA degradation or contamination with RNA. Approximately 1.5 μg of high quality genomic DNA was used to generate fragments of size 300–400 bp by Covaris. Fragments were end-repaired by mixing with End Repair Mix and purified by Ampure XP reagent (Beckman Coulter). These fragments were adenylated and ligated to DNA Adapter Indexes for multiplexing with DNA Ligase Mix. The ligation products were purified and were subsequently enriched by PCR amplification with PCR Master Mix (TrueSeq DNA Sample Prep Kit, Illumina) according to manufacturer’s recommended protocol. The quality and quantity of the genomic DNA library thus obtained was assessed by 2100 Bioanalyzer (Agilent) and real time PCR with Kapa Library Quant Kit (Kapa Biosystems) in ABI 7900HT system (Life Technologies). Genomic DNA library of fragment size between 400 to 500 bp was selected and sequenced on the HiSeq-2000 System (Illumina) using TrueSeq PE Cluster Kit v3 and TrueSeq SBS Kit v3 (Illumina).
3
Whole Genome Shotgun Sequencing Protocols
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Whole genome shotgun DNA library was prepared using Illumina TrueSeq DNA sample preparation kit (FC-121-2001). The paired-end (PE) (2 × 100 nts) sequencing was carried out using Illumina HiSeq 1000 at the Next Generation Genomics Facility at Centre for Cellular and Molecular Platforms (C-CAMP). We prepared whole genome shotgun 454 library for Genotype 1 (GKVK, Bangalore, India) using the rapid library preparation kit from Roche (Cat. No. 05608228001y; version 4.0.12). The 454 sequencing was carried out using GS FLX+ chemistry as per Roche/454 manual instructions (http://454.com ).
4
Whole-Genome Sequencing and RNA-Seq
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Whole-genome shotgun DNA library preparation was performed using the Illumina TrueSeq DNA sample preparation kit (FC-121-2001). The paired-end (PE) (2 × 100 nts) sequencing was carried out using Illumina HiSeq-1000. Also, to increase the size of genome data, we sequenced the genome with paired-end (PE) (2 × 100 nts) using the MGISEQ-2000 platform.
The RNA libraries were prepared using “TruSeq RNA Library Prep Kit v2 from Illumina®” with Illumina standardized protocol. The RNA libraries were quantified on Qubit (dsDNA HS kit) and validated on the TapeStation instrument (D1000 screen tape). These RNA libraries were used for sequencing with the Illumina HiSeq-2500 platform.
The RNA libraries were prepared using “TruSeq RNA Library Prep Kit v2 from Illumina®” with Illumina standardized protocol. The RNA libraries were quantified on Qubit (dsDNA HS kit) and validated on the TapeStation instrument (D1000 screen tape). These RNA libraries were used for sequencing with the Illumina HiSeq-2500 platform.
5
Genetic Variants Discovery via WES and WGS
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Short read high-throughput sequencing was conducted on genomic DNA samples from the family#71342 through Illumina sequencing platforms (Illumina, San Diego, CA) 46 , of which WES on four affected individuals (III:3, IV:4, V:4, V:6) and one unaffected control (V:3) and WGS on two affected (V:4 and V:6) and one unaffected (V:2). Exome was captured using a SureSelect Human All Exome kit (Agilent, Santa Clara, CA) for WES and exome-enriched DNA fragments were sequenced on the illumine Hiseq system (Illumina, San Diego, CA) with a depth of at least 125-fold. The library of WGS was prepared using a trueSeq DNA Sample preparation Kit (Illumina, San Diego, CA) and was sequenced on the library was qualified and then sequenced on the Illumina HiSeq genome analyzer platform (Illumina, San Diego, CA) with an average coverage of 30fold.
6
Illumina DNA Library Preparation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Libraries were prepared with 1 μg of DNA using TrueSeq DNA sample preparation kit (Illumina Cat. No. FC-121-2001). The genomic DNA (1 μg) was fragmented using ultrasonicator (S220: Covaris, USA) to obtain an average of 350 bp fragments. This was followed by end repair, A-tailing, ligation with Illumina adapters, size selection and PCR amplification. The prepared libraries were quantified using Bioanalyzer and quantitative PCR (qPCR). The clusters were generated using cBOT and paired-end sequencing was carried out with Illumina HiSeq 1000 instrument at Center for Cellular and Molecular Platforms (CCAMP), Bangalore, India.
7
Preparation of Illumina DNA Libraries
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA libraries of the three isolates, BS52, D2, and SI, were prepared with 1 µg of DNA using a TrueSeq DNA sample preparation kit (Illumina Cat. No. FC-121-2001). The DNA was fragmented using an ultrasonicator S220 (Covaris, Woburn, MA, USA) to obtain an average of 350 bp fragments. This was followed by end repair, A-tailing, ligation with Illumina adapters, size selection, and PCR amplification. The prepared libraries were quantified using Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and quantitative PCR (qPCR). The clusters were generated using cBOT, and paired-end sequencing was performed using Illumina HiSeq 1000 platform (CCAMP, Bangalore, India). Sequencing data in the form of 2 × 100 bp paired-end reads were obtained. To improve the quality of the assembly, mate-pair sequencing of the D2 isolate was also performed using Illumina HiSeq 1000 platform (CCAMP, Bangalore, India).
8
Whole-genome sequencing of Mtb isolates
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Sequencing of the Mtb isolates was performed at the Genome Institute of Singapore (GIS), Singapore. Genomic libraries were prepared according to the recommendations of the TrueSeq DNA sample preparation kit (Illumina, San Diego, CA). The library pools were subjected to paired-end sequencing on a MiSeq platform (Illumina) generating 250-bp read lengths. The sequence data have been deposited in the Sequence Read Archive (SRA) with the study accession No. SRP071184.
9
Illumina Sequencing of Mycobacterium tuberculosis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Sequencing of the Mtb isolates was performed at the Genome Institute of Singapore, Singapore. Genomic libraries were prepared according to the recommendations of the TrueSeq DNA sample preparation kit (Illumina, San Diego, CA) for the MiSeq platform (Illumina) generating 250-bp read lengths or NEBnext Ultra kit (Illumina, San Diego, CA) for Hiseq (Illumina) platform generating 150-bp read lengths. The sequence data have been deposited in the Sequence Read Archive (SRA) containing 293 biosample accession Nos. SAMN07236248 – 540 under the bioproject accession No. PRJNA390471.
10
Acacia ligulata Whole Genome Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Fresh phyllodes from a seedling of Acacia ligulata Benth. (Fabaceae) were collected from the Western Australian Botanic Garden in Kings Park, Perth. Total genomic DNA was extracted using a CTAB protocol and fragmented with a Covaris S220 focused ultrasonicator. The DNA from A. ligulata was used to construct a 400bp paired-end library using a Trueseq DNA Sample Preparation Kit (Illumina, San Diego, USA), following the manufacturer's directions. The library was clustered on a Rapid Flow Cell v2 (Illumina), using the HiSeq Rapid PE Cluster Kit v2 (Illumina) and on instrument cluster generation on the HiSeq1500 platform, and sequenced using the Hiseq Rapid SBS Kitv2, generating over 4.7 million paired-end reads that passed filter. A PhiX library (Illumina) was spiked in at 1% as a control to provide real time analysis metrics.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!