TY - JOUR
T1 - Exploring the effect of library preparation on RNA sequencing experiments
AU - Wang, Lei
AU - Felts, Sara J.
AU - Van Keulen, Virginia P.
AU - Pease, Larry R.
AU - Zhang, Yuji
N1 - Funding Information:
The authors would like to acknowledge the scientists and staff of the Mayo Clinic Medical Genome Facility Gene Expression Core for all library preparation, data acquisition and processing through their RNAseq pipeline. This project was supported by the National Cancer Institute grant P30 CA134274 to the University of Maryland Baltimore.
Funding Information:
The authors would like to acknowledge the scientists and staff of the Mayo Clinic Medical Genome Facility Gene Expression Core for all library preparation, data acquisition and processing through their RNAseq pipeline. This project was supported by the National Cancer Institute grant P30 CA134274 to the University of Maryland Baltimore. The authors declare that they have no competing interests.
Funding Information:
The authors would like to acknowledge the scientists and staff of the Mayo Clinic Medical Genome Facility Gene Expression Core for all library preparation, data acquisition and processing through their RNAseq pipeline. This project was supported by the National Cancer Institute grant P30 CA134274 to the University of Maryland Baltimore.
Publisher Copyright:
© 2018
PY - 2019/12
Y1 - 2019/12
N2 - RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect of sample preparation factors on its analytical reliability using patient samples. In this study, we examined the impact of three major sample preparation factors (i.e., cDNA library storage time, the quantity of input RNA, and cryopreservation of cell samples) on sequence biases, gene expression profiles, and enriched biological functions using RNAs isolated from primary B cell and CD4+ cell blood samples of healthy subjects. Our comprehensive comparison results suggested that different cDNA library storage time, quantity of input RNA, and cryopreservation of cell samples did not significantly alter gene transcriptional expression profiles generated by RNA-seq experiments. These findings shed new lights on the potential applications of RNA-seq technique to patient samples in a regular clinical setting.
AB - RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect of sample preparation factors on its analytical reliability using patient samples. In this study, we examined the impact of three major sample preparation factors (i.e., cDNA library storage time, the quantity of input RNA, and cryopreservation of cell samples) on sequence biases, gene expression profiles, and enriched biological functions using RNAs isolated from primary B cell and CD4+ cell blood samples of healthy subjects. Our comprehensive comparison results suggested that different cDNA library storage time, quantity of input RNA, and cryopreservation of cell samples did not significantly alter gene transcriptional expression profiles generated by RNA-seq experiments. These findings shed new lights on the potential applications of RNA-seq technique to patient samples in a regular clinical setting.
KW - Cryopreservation
KW - Library storage time
KW - Quantity of input RNA
KW - RNA-seq
KW - lincRNA
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U2 - 10.1016/j.ygeno.2018.11.030
DO - 10.1016/j.ygeno.2018.11.030
M3 - Article
C2 - 30529531
AN - SCOPUS:85057957895
SN - 0888-7543
VL - 111
SP - 1752
EP - 1759
JO - Genomics
JF - Genomics
IS - 6
ER -