V2 kits

Manufactured by Illumina

Sourced in United States

The V2 kits are a set of reagents and consumables designed for use with Illumina sequencing instruments. These kits provide the necessary components to perform library preparation and sequencing reactions. The core function of the V2 kits is to enable the generation of high-quality sequencing data from DNA or RNA samples.

Automatically generated - may contain errors

Lab products found in correlation

Kapa library preparation hyper plus kit, by Roche (2 mentions) Nextgene software, by SoftGenetics (2 mentions) Seqcap ez choice library, by Roche (2 mentions) Cobas dna sample preparation kit, by Roche (1 mentions) Miseq desktop, by Illumina (1 mentions) Dna sample preparation kit, by Roche (1 mentions)

4 protocols using v2 kits

Comprehensive Mutation Analysis of Paraffin-Embedded Tissues

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The DNA was extracted from paraffin-embedded tissue blocks by the Cobas DNA Sample Preparation Kit (Roche) according to manufacturer’s protocol. Mutation analysis was performed by multiparallel sequencing (NGS). Indexed Illumina NGS library was constructed from 100 ng tumor DNA by KAPA Library Preparation Hyper Plus Kit (Kapa Biosystems). Hybrid selection was performed with a custom SeqCap EZ Choice Library (Roche NimbleGen). The library was designed using genome build hg19 NCBI. Build 37.1/GRCh37 input genomic regions are listed as follows: AKT, BRAF (exons 11,15), BRCA1, BRCA2, EGFR (exons 18, 19, 20, 21), ESR, GNAS (exon 8), KRAS, KIT, MLH1, MSH2, MSH6, NRAS, PDGFRA (exons 8, 10, 12, 14, 18), PIK3CA, PMS2, PTEN, RET and TP53.
Paired-end cluster generation and sequencing were performed according to standard protocols from Illumina, using v2 kits. Sequencing data analysis and variant classification were performed by NextGENe software (Softgenetics) with minimum 5% variant allele frequency filtering.

Skarkova V., Vitovcova B., Matouskova P., Manethova M., Kazimirova P., Skarka A., Brynychova V., Soucek P., Vosmikova H, & Rudolf E. (2022). Role of N-Cadherin in Epithelial-to-Mesenchymal Transition and Chemosensitivity of Colon Carcinoma Cells. Cancers, 14(20), 5146.

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Metagenomic Analysis of Bacterial Samples

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DNA isolated from BS and RS samples was used for metagenomic analysis. These samples were processed and sequenced with Shotgun using Illumina ^® MiSeq desktop using the 2 × 250 bp paired-end reagent V2 Kits (Illumina ^®, United States) technology with a standard quantification pattern. Bioinformatic analysis and quality control were performed using the Fast QC tool (Andrews, 2017 ). Q-score was used to predict the probability of an error in base-calling. Over 75% of bases > Q30 averaged across the entire run was considered acceptable. Raw sequence reads underwent quality trimming using Trimmomatic to remove adaptor contaminants and low-quality reads (Li et al., 2010 (link)).

González D., Robas M., Fernández V., Bárcena M., Probanza A, & Jiménez P.A. (2022). Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén. Frontiers in Microbiology, 13, 797444.

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Nationwide SARS-CoV-2 Genome Sequencing

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With the aim of generating a random sample of viral infections across the entire country, a total of 213 samples were retrieved from six major hospitals in Israel spanning the entire geography of Israel from south to north (Table 1 and Supplementary Table 2).Table 1

Summary of samples successfully sequenced.

a
Age group
Age group	Number of samples
0–9	8
10–19	17
20–29	42
30–39	28
40–49	26
50–59	29
60–69	31
70-79	15
80–89	11
90 and up	3
Unknown	2

b
Location and hospital
Hospital	Geographic region	Number of samples
Barzilai Medical Center	South coast district	30
Samson Assuta Ashdod University Hospital	South coast district	23
Hadassah University Hospital - Ein Kerem	Jerusalem district	62
Poria Medical Center	North district	26
Sheba Medical Center	Tel-Aviv district	51
Soroka Medical Center	South district	20

c
Sex	Number of samples
Female	101
Male	111

The table is divided by metadata information (a–c). Source data are provided as a Source Data file.

We obtained RNA extracted from nasopharyngeal samples. Sequencing was performed based on the V3 Artic protocol (https://artic.network/ncov-2019). Briefly, reverse transcription and multiplex PCR of 109 amplicons was performed, and adapters were ligated to allow for sequencing. All samples were run on an Illumina Miseq using 250-cycle V2 kits in the Technion Genome Center (Israel). Supplementary Table 13 contains all primer names and sequences as described in the Artic protocol.

Miller D., Martin M.A., Harel N., Tirosh O., Kustin T., Meir M., Sorek N., Gefen-Halevi S., Amit S., Vorontsov O., Shaag A., Wolf D., Peretz A., Shemer-Avni Y., Roif-Kaminsky D., Kopelman N.M., Huppert A., Koelle K, & Stern A. (2020). Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nature Communications, 11, 5518.

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Targeted NGS Profiling of Common Oncogenes

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DNA was extracted from formalin-fixed, paraffin embedded tumour tissue after deparaffinization in xylene and rehydration in ethanol using the commercial DNA Sample Preparation Kit (Roche, Basel, Switzerland) according to the manufacturer's protocol. Mutation analysis was performed by Massively Parallel Sequencing (NGS). Indexed Illumina NGS library was constructed from 100 ng tumour cell line DNA using KAPA Library Preparation Hyper Plus Kit (Kapa Biosystems). Hybrid selection was performed with a custom SeqCap EZ Choice Library (Roche NimbleGen). The library was designed using the genome build hg19 NCBI Build 37.1/GRCh37 (input genomic regions: KRAS NM_004985.4 -full coding regions; NRAS NM_002524.4 -full coding regions; BRAF NM_004333.4 -exons 11 a 15; PTEN NM_000314.4 -full coding regions). Paired-end cluster generation and sequencing were performed according to standard protocols from Illumina, using v2 kits. Sequencing data analysis and variant annotation was performed using NextGENe software (Softgenetics) with minimum 5% variant allele frequency filtering.

Krbal L., Soukup J., Stanislav J, & Hanusova V. (2017). Derivation and basic characterization of colorectal carcinoma primary cell lines. Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia, 161(4).

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