Transcriptome Meta Data Compilation for Chinese hamster tissues and CHO cell lines

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http://dx.doi.org/10.13020/D6JS3F
https://hdl.handle.net/11299/180904

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Keywords

transcriptome

RNA-Seq

Microarray

Chinese hamster ovary

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Transcriptome Meta Data Compilation for Chinese hamster tissues and CHO cell lines

Published Date

2016-06-06

Authors

Vishwanathan, Nandita

Yongky, Andrew

Johnson, Kathryn C

Fu, Hsu-Yuan

Jacob, Nithya M

Le, Huong

Bandyopadhyay, Arpan

Group

University of Minnesota Department of Chemical Engineering and Material Sciences, Hu Group

Author Contact

Hu, Wei-Shou
wshu@umn.edu

Type

Dataset
Genomics Data

Abstract

Transcriptomics is increasingly being used on Chinese hamster ovary (CHO) cells to unveil physiological insights related to their performance during production processes. The rich transcriptome data can be exploited to provide impetus for systems investigation such as modeling the central carbon metabolism or glycosylation pathways, or even building genome-scale models. To harness the power of transcriptome assays, we assembled and annotated a set of RNA-Seq data from multiple CHO cell lines and Chinese hamster tissues, and constructed a DNA microarray. These tools were used to measure the transcript expression of tissues (liver, brain, ovary), 3 parental cell lines (DG44, DXB11, CHO-K1) and 16 recombinant cell lines. Transcript expression levels for tissues and cell lines have been compiled as an excel spreadsheet to allow for a rapid survey of transcript levels of different genes.

Description

The data is organized in the speadsheet file named Transcriptome Meta Data.xlsx and has been color coded for easy visualization. Gene information contains gene description, symbol and orthologous mouse ENSEMBL identifiers. Columns in pink pertaining to 26 different functional pathways can be sorted for the value 1 to quickly assess expression of genes in that pathway. This is followed by RNA sequencing and microarray expression data for tissues and cell lines. The minimum, mean and maximum expression values of each gene for all the cell lines in both microarray and sequencing datasets have also been included.

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Data Repository for U of M (DRUM)

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Vishwanathan, Nandita; Yongky, Andrew; Johnson, Kathryn C; Fu, Hsu-Yuan; Jacob, Nithya M; Le, Huong; Bandyopadhyay, Arpan. (2016). Transcriptome Meta Data Compilation for Chinese hamster tissues and CHO cell lines. Retrieved from the Data Repository for the University of Minnesota (DRUM), http://dx.doi.org/10.13020/D6JS3F.

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