Apr 14, 2025

Public workspaceJAX-Sen: Library construction using KAPA RNA HyperPrep Kit for Bulk RNAseq

DOI
https://dx.doi.org/10.17504/protocols.io.kxygx7pjwl8j/v1
  • Christine Goldfarb1,
  • Jennifer Idol1,
  • Rahul Maurya1,
  • chewyee.ngan 1,
  • Mark Adams1
  • 1The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  • Cellular Senescence Network (SenNet) Method Development Community
Harshpreet Chandok
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DOI: https://dx.doi.org/10.17504/protocols.io.kxygx7pjwl8j/v1
Protocol Citation: Christine Goldfarb, Jennifer Idol, Rahul Maurya, chewyee.ngan , Mark Adams 2025. JAX-Sen: Library construction using KAPA RNA HyperPrep Kit for Bulk RNAseq. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygx7pjwl8j/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 14, 2025
Last Modified: April 14, 2025
Protocol Integer ID: 126680
Keywords: kapa rna hyperprep kit for bulk rnaseq, kapa rna hyperprep kit with riboerase, using kapa rna hyperprep kit, kapa rna hyperprep kit, sequence libraries fro bulk rnaseq, bulk rnaseq, rna, sequence libraries fro, riboerase, roche for library construction, library construction, library
Funders Acknowledgements:
National Institute on Aging (NIA) JAX-Sen Senescence Tissue Mapping Center Grant
Grant ID: U54 AG079753
Abstract
This protocol describes the methods and procedures used to construct and sequence libraries fro bulk RNAseq using KAPA RNA HyperPrep Kit with RiboErase (HMR) from Roche for library construction and NovaSeq X Plus from Illumina.
Troubleshooting
Procedure
The input parameters process workflow and library construction for the KAPA RNA HyperPrep Kit
for Illumina platforms is mentioned below:
https://rochesequencingstore.com/wp-content/uploads/2017/10/KAPA-RNA-HyperPrep-Kit-1.pdf

Indexes used are IDT for Illumina – TruSeq DNA UD Indexes v2 (96 Indexes, 96 Samples) #20040870
https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_truseq_dna_pcr_free_sample_prep.pdf
The NovaSeq X Plus from Illumina is used for sequencing. Sequencing on this instrument is on a patterned flow cell with two color chemistry (green and blue). Sequencing is on a 10B Flow Cell with 8 lanes and can currently be done in 100 cycles, 200 cycles or 300 cycles. Note that each cycle kit comes with 38 cycles to account for index reads. Each lane yields 1250M reads.