|
| Status |
Public on Jun 12, 2018 |
| Title |
Abdominal Aorta (Injured) 48HR Experimental Batch 2 MouseID E2A |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Aorta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Abdominal Aorta
segment: Injured Segment
time point: 48HR 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 |
Inj48hrE2A
|
| 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 |
SAMN09394379 |
| SRA |
SRX4193336 |
