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Series GSE127171 Query DataSets for GSE127171
Status Public on Apr 01, 2019
Title Spatially patterned scaffolds enhances vascular organization and functional integration in volumetrc muscle loss
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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
Contributor(s) Huang NF, Nakayama KH
Citation(s) 31098403
Submission date Feb 26, 2019
Last update date Jul 03, 2019
Contact name Ngan Huang
Phone 5108476870
Organization name Stanford University
Department Cardiothoracic Surgery
Lab Huang Lab
Street address 3801 Miranda Avenue
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL25526 Illumina NovaSeq 6000 (Homo sapiens; Mus musculus)
Samples (11)
GSM3629664 1RM1HUA
GSM3629665 2RM2HUA
GSM3629666 3RM3HUA
BioProject PRJNA524279
SRA SRP186857

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Supplementary file Size Download File type/resource
GSE127171_Normalized_counts_Qluo_v1.txt.gz 855.4 Kb (ftp)(http) TXT
GSE127171_diffgene_AC_vs_RC_gsea_rank.xlsx.gz 397.0 Kb (ftp)(http) XLSX
GSE127171_diffgene_AM_vs_RM_gsea_rank.xlsx.gz 397.8 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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