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SRX5430896: GSM3629666: 3RM3HUA; Mus musculus; RNA-Seq
2 ILLUMINA (Illumina NovaSeq 6000) runs: 45.3M spots, 13.6G bases, 3.8Gb downloads

Submitted by: NCBI (GEO)
Study: Spatially patterned scaffolds enhances vascular organization and functional integration in volumetrc muscle loss
show Abstracthide Abstract
We report the application of bioengineered skeletal muscle composed of murine skeletal myoblasts interspersed with human vascular endothelial cells (ECs) using spatially patterned scaffolds for the treatment of volumetric muscle loss. To gain insights into the molecular mechanisms by which spatial patterning promoted myo-angiogenesis, we performed mRNA sequencing of engineered muscle and endothelialized engineered muscle on either randomly-oriented or aligned scaffolds. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from four groups: 1) randomly-oriented scaffold seeded with myoblasts; 2) randomly-oriented scaffolds seeded with myoblasts + ECs; 3) aligned scaffold seeded with myoblasts only; 4) aligned scaffold seeded with myoblasts + ECs. Samples were generated in triplicate and the NovaSeq 6000 (Illumina) sequencing platform was utilized. 150-bp paired-end reads were generated (20-30 million reads per sample). The raw data were checked for quality with FastQC (Version 0.11.7) and results were aggregated with MultiQC and were aligned to the mouse genome (GRCm38) using STAR (Version 2.5.3a) with ENCODE options for long RNA-seq pipeline. The alignment results were assessed using Samtools and aggregated with MultiQC (Version 1.5) and the differential gene expression analysis of the uniquely mapped reads/raw counts wwas performed using the DESeq2 package (Version 1.20.0). Each DE analysis was composed of a pairwise comparison between an experimental group and the control group. Differentially expressed genes were identified after false discovery rate (FDR = 0.05) correction. Overall design: Examination of differences in transcriptome profiling between 4 different bioengineered skeletal muscle
Sample: 3RM3HUA
SAMN11020144 • SRS4410891 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was isolated from cell lysates from engineered muscle and endothelialized engineering muscle on randomly-oriented or aligned scaffolds (n=3) according to the manufacture's protocol (GeneJet RNA Purification Kit, Thermo Fisher). At least 1000ng of total RNA was pelleted per sample. Library preparation and RNA Sequencing was performed by Novogene Corporation using the NovaSeq 6000 (Illumina) sequencing platform, and 150-bp paired-end reads were generated (20-30 million reads per sample). Briefly, RNA integrity was assessed (RNA Nano 6000 Assay Kit, Bioanalyzer 2100, Aligent Technologies, CA) and 3ug RNA per sample was used to generate sequencing libraries (NEBNext Ultra RNA Library Prep Kit for Illumina) according to manufacturer's recommendations. Library fragments were purified (AMPure XP system, Beckman Coulter, Beverly) to select cDNA fragments (150-200 bp in length). PCR was performed with Phusion High-Fidelity DNA polymerase, and purified by the AMPure XP system and assessed for quality on the Agilent Bioanalyzer 2100 system.
Experiment attributes:
GEO Accession: GSM3629666
Links:
Runs: 2 runs, 45.3M spots, 13.6G bases, 3.8Gb
Run# of Spots# of BasesSizePublished
SRR863210722,677,4496.8G1.9Gb2019-04-01
SRR863210822,589,6886.8G1.9Gb2019-04-01

ID:
7338596

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