|
| Status |
Public on Aug 21, 2019 |
| Title |
DTR-PBS-388U |
| Sample type |
SRA |
| |
|
| Source name |
heart, ventricles
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart, ventricles
Sex: Male
age (weeks): 10
strain: C57BL/6
treatment: diphtheria toxin-mediated injury; vehicle (PBS-treated)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hearts were removed and ventricular apexes were flash-frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the standard Ensembl gtf annotation and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and human-Mfn2 cDNA), using tophat v2.1.1.
htseq-count (authored by Simon Anders) was used in union mode to assign tophat-aligned reads to gene entries in the standard Ensembl gtf annotation supplied with the bowtie2 iGenome.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Genome_build: GRCm38 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each gene. Depth-normalized values were calculated according to DESeq’s library normalization algorithm.
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Aug 21, 2019 |
| Contact name |
Scot J Matkovich |
| E-mail(s) |
smatkovich@gmail.com
|
| Organization name |
Washington University School of Medicine
|
| Department |
Center for Cardiovascular Research
|
| Street address |
660 S Euclid Ave, box 8086
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE116988 |
Transcriptional profile of injured hearts treated with the cholinesterase inhibitor pyridostigmine (PYR) at Day 5 |
|
| Relations |
| BioSample |
SAMN09650228 |
| SRA |
SRX4384301 |
