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. 2021 May 12:36:107130.
doi: 10.1016/j.dib.2021.107130. eCollection 2021 Jun.

Human Chr18 transcriptome dataset combined from the Illumina HiSeq, ONT MinION, and qPCR data

George Krasnov  1   2   3 , Timur Shkrigunov  1 , Sergey Radko  1 , Konstantin Ptitsyn  1 , Valeriya Shapovalova  4 , Olga Timoshenko  1 , Svetlana Khmeleva  1 , Leonid Kurbatov  1 , Yana Kiseleva  5 , Ekaterina Ilgisonis  1 , Olga Kiseleva  1 , Igor Vakhrushev  1 , Anastasia Tsvetkova  1 , Ivan Buromski  6 , Sergey Markin  1 , Alexander Archakov  1 , Andrey Lisitsa  1 , Elena Ponomarenko  1
Affiliations

Human Chr18 transcriptome dataset combined from the Illumina HiSeq, ONT MinION, and qPCR data

George Krasnov et al. Data Brief. .

Abstract

The chromosome-centric dataset was created by applying several technologies of transcriptome profiling. The described dataset is available at NCBI repository (BioProject ID PRJNA635536). The dataset referred to the same type of tissue, cell lines, transcriptome sequencing technologies, and was accomplished in a period of 8 years (the first data were obtained in 2013 while the last ones - in 2020). The high-throughput sequencing technologies were employed along with the quantitative PCR (qPCR) approach, for data generation using the gene expression level assessment. qPCR was performed for a limited group of genes, encoded on human chromosome 18, for the Russian part of the Chromosome-Centric Human Proteome Project. The data of high-throughput sequencing are provided as Excel spreadsheets, where the data on FPKM and TMP values were evaluated for the whole transcriptome with both Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing.

Keywords: HepG2; Human proteome project; Illumina HiSeq; Liver tissue; Oxford nanopore Technologies; Transcriptome.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article.

Figures

Fig. 1
Fig. 1
Dataset origin and structure. Quantitative data for samples of liver tissue and HepG2 cells from several datasets, obtained in 2013 and 2020 with SOLiD, Illumina GII/HiSeq, qPCR and Oxford Nanopore (MinION), and mapped to the Chr18-encoded proteins.
Fig. 2
Fig. 2
Relationships between clusters within dataset. Each leaf in the dendrogram corresponds to the certain source of the data about the expression level of Chromosome 18 genes, measured with different methods and processed with different bioinformatics pipelines (bowtie2-RSEM..RefSeq, Salmon, bowtie2-RSEM, STAR-RSEM, Salmon..Gencode, Tophat-Cufflinks, Salmon..Ensembl).
See this image and copyright information in PMC

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