Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Selection of RNA-seq library preparation protocol for a comprehensive transcriptome analysis in T acute lymphoblastic leukemia (T-ALL)

ABSTRACT: The aim of this study was to compare two different library preparation protocols: Illumina TruSeq Stranded mRNA (referred to as PA) and TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (RD) each with two different variants of the fragmentation step: standard fragmentation conditions (94°C for 8 minutes; further described as P1) and modified conditions (90°C for 2 minutes; further described as P2). The modification was expected to produce longer fragments. Each of the 5 tested T-ALL samples was sequenced using a combination of 4 different protocols: PA_P1, RD_P1, PA_P2, RD_P2 (for PA_P2 we performed two technical replicates). All 25 libraries were sequenced on Illumina NovaSeq6000 platform, in 2x150 mode, with a coverage of 150M reads/sample. High number of reads obtained for each of the samples allowed us to carry out a comprehensive comparison using various analysis methods aimed at identifying differentially expressed genes, alternative splicing events, gene fusions, somatic mutations and indels.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Małgorzata Dawidowska

PROVIDER: E-MTAB-10253 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

RNA-seq library preparation for comprehensive transcriptome analysis in cancer cells: The impact of insert size.

Jaksik Roman R Drobna-Śledzińska Monika M Dawidowska Małgorzata M

Genomics 20211103 6

With long reads and high coverage, RNA-seq enables comprehensive transcriptome analysis of cancer cells, provided that optimal length of libraries (and their inserts) is assured, to avoid overlap of paired reads and consequent loss of sequencing data. We assessed TruSeq Stranded library preparation protocols (poly(A) enrichment-PA and rRNA depletion-RD) for the thoroughness of transcriptome analysis of a heterogeneous cancer, acute lymphoblastic leukemia. We applied 2x150PE sequencing, >150 M re ...[more]

PMID: 34740778

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Dataset Information

Selection of RNA-seq library preparation protocol for a comprehensive transcriptome analysis in T acute lymphoblastic leukemia (T-ALL)

Publications

RNA-seq library preparation for comprehensive transcriptome analysis in cancer cells: The impact of insert size.

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