NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3185108 Query DataSets for GSM3185108
Status Public on Jun 12, 2018
Title Abdominal Aorta (Injured) 03HR Experimental Batch 3 MouseID C3B
Sample type SRA
 
Source name Mouse Aorta
Organism Mus musculus
Characteristics tissue: Abdominal Aorta
segment: Injured Segment
time point: 03HR post-injury
strain: C57BL6/J
Treatment protocol Aortae were wounded using mechanical pressure. See Shirali et al, JOvE, 2016 (PMID: 27911412) for details.
Extracted molecule total RNA
Extraction protocol RLT buffer (Qiagen RNEasy kit) flush through lumen of vessel; for "tissue" fraction, RNA was extracted from homogenized post-flush vessel. See Briot et al, Dev Cell, 2014 (PMID: 25535917) for details.
Library construction was performed using the NuGEN Oviation Ultralow Library V2 kit according to manufacturer's recommended protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Inj00hrC3B
Data processing Alignment: HISAT 2.0.3 default parameters per Galaxy server 16.10, excepting: (use ENSEMBL GTF file with known splice sites for spliced alignment)
Generation of Raw Counts: Htseq-count 0.6.1galaxy3, default parameters per Galaxy server 16.10
Count normalization and testing for differential expression: DESeq2 1.14.1, default parameters
Genome_build: Mus_musculus GRCm38.84 (from ENSEMBL - http://www.ensembl.org/Mus_musculus/Info/Annotation)
Supplementary_files_format_and_content: Excel file containing: 1) Regularized log values of transcripts counts for each sample 2) Normalized counts for each sample and 3) Pairwise comparisons between each set of samples
 
Submission date Jun 11, 2018
Last update date Jun 12, 2018
Contact name Feiyang Ma
Organization name UCLA
Department Molecular Biology Institute
Lab Pellegrini Lab
Street address 610, Charles Young Dr East, TLSB 3000C
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL21493
Series (1)
GSE115618 Comparison of global gene expression in homeostatic and regenerating endothelium of the adult mouse aorta
Relations
BioSample SAMN09394390
SRA SRX4193355

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap