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| Status |
Public on May 04, 2020 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and LDB2-/- skin epidermal lysates |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived mouse back skin epidermal transcriptome profiling (RNA-seq) to evaluate protocols for optimal high-throughput data analysis
Methods: Total RNA was isolated using an RNeasy Kit (Qiagen, Germantown, MD, USA). The mRNA sequence libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit(RS-122; Illumina, San Diego, CA, USA). The protocols followed the TruSeq Stranded mRNA Sample Preparation Guide (Part 15031047 Rev. E). Sequencing was performed using an Illumina Novaseq 6000 sequencer (101 bp paired-end runs), NovaSeq 6000 System User Guide Document (#1000000019358 v02), and TruSeq Stranded mRNA LT Sample Prep Kit. After removing low-quality and adapter sequences, sequence reads were aligned to the University of California–Santa Cruz(UCSC mm10), mouse genome reference sequence Mus musculus(RefSeq_2017_06_12) using Hierarchical Indexing for Spliced Alignment of Transcripts HISAT2 version 2.1.0, Bowtie2 2.3.4.1
Results: StringTie v.1.3.4d was used to estimate gene abundance. Abundance was measured in fragments per kilobase of exon per million fragments mapped; any values of 0 were discarded. To establish log2 transformation, 1 was added to each abundance value of filtered genes, and quantile normalization was performed.
Conclusions: Our study represents detailed analysis of Skin epidermal lysates transcriptomes, with biologic replicates, generated by mRNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a tissue. We conclude that mRNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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| Overall design |
Back skin epidermal lysates mRNA profiles of 63-day old wild type (WT) and LDB2-/- mice were generated by deep sequencing, in duplicate, using Illumina Novaseq 6000.
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| Citation missing |
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| BioProject |
PRJNA553650 |
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| Submission date |
Jul 24, 2019 |
| Last update date |
May 04, 2020 |
| Contact name |
Jonghyo Lim |
| Organization name |
Yonsei university
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| Department |
Biochemistry
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| Lab |
Vascular Genomics laboratory
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| Street address |
Yonsei-ro 50
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| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| Relations |
| SRA |
SRP214021 |
| SRA |
SRP216225 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE134785_Normalized_FPKM.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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