RNA sequencing was performed using the TruSight RNA Pan-Cancer panel (Illumina, San Diego, CA) which contains 1385 cancer genes and enables fusion calling and variant detection within the panel. Twenty nanograms of RNA was processed according to the manufacturer’s protocol and was sequenced on a Next Seq 550 system (Illumina, San Diego, CA) using the NextSeq® Reagent Kit v3 (150 cycles) with a PE NextSeq® Flow Cell. Data analyses were performed using the Illumina BaseSpace apps TopHat Alignment (version 1.0.0, read mapping on hg19 reference genome by TopHat21, fusion calling by TopHat-Fusion2) and RNA-seq Alignment (version 1.1.0, read mapping on hg19 reference genome by STAR3, fusion calling by Manta4 using standard settings) (BaseSpace.illumina.com/apps">https://BaseSpace.illumina.com/apps ). Fusion transcripts with a low number of split-reads were excluded as likely false positives. The raw data of the sequence variants were converted to variant call format (vcf) files and analysed in Variant Studio software v.4.0.
Pe nextseq flow cell
Manufactured by Illumina
The PE NextSeq® Flow Cell is a key component of the NextSeq® 550 System, a high-throughput DNA sequencing platform. It serves as the sample holder and reaction chamber for the sequencing process, enabling the efficient generation of sequencing data from DNA samples.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using pe nextseq flow cell
1
Comprehensive Cancer Gene Profiling via Illumina RNA Sequencing
2
RNA Sequencing Pipeline for Pan-Cancer Profiling
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RNA sequencing was performed using the TruSight RNA Pan-Cancer panel (Illumina, San Diego, CA) on a Next Seq 550 system (Illumina, San Diego, CA) using NextSeq® Reagent Kit v3 (150 cycles) with a PE NextSeq® Flow Cell. Data analysis was performed using the Illumina BaseSpace apps TopHat Alignment (version 1.0.0, read mapping on hg19 reference genome by TopHat21, fusion calling by TopHat-Fusion2, and RNA-seq Alignment (version 1.1.0, read mapping on hg19 reference genome by STAR3, fusion calling by Manta4 using standard settings (https://basespace.illumina.com/apps ). Raw data of sequence variants were analyzed in Variant Studio software v.4.0.
A detailed description of all methods can be found in the online Supplementary materials.
A detailed description of all methods can be found in the online Supplementary materials.
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