Small-scale sequencing was performed using the Illumina MiSeq system with the reagent kit version 3 (150 cycles) and the reagent nano kit version 2 (300 cycles) (San Diego, CA, USA), with some modifications for denaturation and neutralization of the library, as described previously (8 (link)). The amount of input library varied depending on the purpose of the experiments. Large-scale sequencing using the HiSeq X Ten and NovaSeq 6000 were performed by Macrogen Japan Corp. (Kyoto, Japan) as commercial services. Sequenced reads were delivered to us after demultiplexing of indexed libraries.
Reagent kit version 3
Manufactured by Illumina
Sourced in United States
The Reagent kit version 3 is a set of chemical reagents and consumables designed for use with Illumina's sequencing platforms. It contains the necessary components to prepare DNA samples for sequencing, including enzymes, buffers, and other necessary reagents. The core function of this product is to enable the library preparation and sequencing workflow for Illumina's sequencing instruments.
Automatically generated - may contain errors
2 protocols using reagent kit version 3
1
Small and Large-scale Sequencing Protocols
2
Targeted NGS and RNA Sequencing for Myeloid Neoplasms
Check if the same lab product or an alternative is used in the 5 most similar protocols
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Next-generation sequencing (NGS) analysis of genomic samples for somatic pathogenic variants was performed using the TruSight myeloid panel (Illumina, San Diego, CA) library kit followed by sequencing on a MiSeq instrument using reagent kit version 3 (Illumina, San Diego, CA). Variants were called using Ingenuity Variant analysis and QIAGEN Clinical Insight (QCI) Interpret (QIAGEN, Hilden, Germany). Details of the genes and exons included in the panel are listed in Supplementary Table 1. Details regarding filtering of variants are available upon request.
Targeted sequencing of RNA for the evaluation of RUNX1 gene fusions was performed using the Archer TM FusionPlex TM Heme Panel v2 for the Illumina Platform. Library preparation was carried out according to the manufacturer's instructions (ArcherDX, Boulder, CO) and 200 ng total RNA was used as input material. Libraries were sequenced by pooling four samples, at a concentration of 18 pM, using sequencing kit version 2 on a MiSeq instrument (Illumina, San Diego, CA). RUNX1 fusions were assessed using Archer analysis software version 6.0.3.2 (ArcherDX, Boulder, CO).
Targeted sequencing of RNA for the evaluation of RUNX1 gene fusions was performed using the Archer TM FusionPlex TM Heme Panel v2 for the Illumina Platform. Library preparation was carried out according to the manufacturer's instructions (ArcherDX, Boulder, CO) and 200 ng total RNA was used as input material. Libraries were sequenced by pooling four samples, at a concentration of 18 pM, using sequencing kit version 2 on a MiSeq instrument (Illumina, San Diego, CA). RUNX1 fusions were assessed using Archer analysis software version 6.0.3.2 (ArcherDX, Boulder, CO).
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