Edd2e08f-3760-44a7-8559-95963d261a25 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009706 | EGA |
REPOSITORIES: EGA
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2024-07-15 | E-MTAB-13225 | biostudies-arrayexpress
Project description:RNA sequencing analysis was performed on mouse cell samples. Quality control of total RNA samples after RNA isolation with the Agilent Bioanalyzer revealed acceptable RNA quality for 12 out of 30 provided samples. Libraries were successfully prepared from these RNA samples using the Illumina TruSeq® Stranded mRNA technology. This approach uses fragmentation and sequencing adapter ligation in combination with a poly-T oligo pulldown. RNA sequencing was performed on the Illumina NextSeq500 next generation sequencing system (Illumina) and its high output mode with two runs of 1x75 bp single-end read chemistry and a high amount of high quality reads was generated.
2021-07-07 | E-MTAB-9353 | biostudies-arrayexpress
Project description:RNA sequencing analysis was performed on at least 1000 tumor-derived bulk-sorted mouse cells. Quality control of total RNA samples after RNA isolation with the Agilent Bioanalyzer revealed acceptable RNA quality for provided samples. Libraries were successfully prepared from these RNA samples using the Illumina TruSeq® Stranded mRNA technology. This approach uses fragmentation and sequencing adapter ligation in combination with a poly-T oligo pulldown. RNA sequencing was performed on the Illumina NextSeq500 next generation sequencing system (Illumina) and its high output mode with two runs of 1x150 bp single-end read chemistry and a high amount of high quality reads was generated.
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Project description: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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