|
| Status |
Public on Nov 16, 2020 |
| Title |
ctrl12 |
| Sample type |
SRA |
| |
|
| Source name |
Prox1-eGFP
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart
strain: C57BL/6
cell type: cardiomyocytes
treatment: Control
age (months): 16
animal id: 9
sequencing batch: batch3
|
| Treatment protocol |
Angiotensin II infusion was used to induce chronic cardiac dysfunction and VEGFCc156s, a lymphangiogenic therapy, was infused concomintantly with angiotensin II as a treatment for some of the animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cardiomyocytes, lymphatic endothelial cells and blood endothelial cells were isolated from mouse heart and lymphatic endothelial cells were isolated from mouse diaphragm using an optimized protocol with FACS
Total RNA was converted into cDNA using the Smart-Seq ultra low input RNA kit and cDNA was converted into libraries using Nextera DNA XT Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
3-D
|
| Data processing |
Reads were assessed for quality and aligned to the GRCm38 mus musculus genome using STAR (v.2.5.3a) with these options selected: --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90 --alignIntronMax 1000000. Quantmode TranscriptomeSam was also selected to allow for input to Salmon for read counts
Aligned reads were quantified using Salmon (v.0.12.0) in alignment-based mode with gcBias option selected and mapped to the Ensembl 95 mus musculus gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing gene summarized TPM values, with samples across columns and genes, given by ensembl identifiers, by row
|
| |
|
| Submission date |
May 07, 2020 |
| Last update date |
Nov 16, 2020 |
| Contact name |
Michael Nagle |
| E-mail(s) |
michael.nagle@pfizer.com
|
| Organization name |
Pfizer
|
| Department |
Internal Medicine Research Unit
|
| Street address |
1 Portland Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02140 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE150041 |
RNA sequencing study using Prox1-eGFP mice to investigate the role of lymphatic vasculature in chronic cardiac dysfunction |
|
| Relations |
| BioSample |
SAMN14848518 |
| SRA |
SRX8287716 |
