|
| Status |
Public on Feb 22, 2019 |
| Title |
WT rep1 |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
organ: heart
age: 86-week-old
genotype: wt
gender: female
experiment: A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
heart were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Fibrous RNAeasy kit.
Experiment A was constructed with Ion Total RNA-Seq Kit v2 and Experiment B was prepared with Illumina TruSeq RNA Stranded mRNA HT Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
IonXpressRNA_010_165_WT_1
|
| Data processing |
Experiment A was aligned to mm10 by the Ion Torrent Suite and Experiment B was aligned to the reference genome mm10 by STAR v2.6.0c
Experiment A was quantified by ENSEMBL annotations and normalized using Deseq algorithm by the StrandNGS program
Experiment B was qunatified using ENSEMBLv93 annotations and normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization (-v0.8.5b-beta)
Genome_build: mm10
Supplementary_files_format_and_content: For experiment A, tab-delimited text file with transcript-level read counts. For experiment B, tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Feb 22, 2019 |
| Contact name |
Jeffrey Field |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennsylvania
|
| Department |
Pharmacology
|
| Street address |
1313 BRB II/III U
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104-6084 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE125603 |
Targeting MRTF/SRF in CAP2-dependent dilated cardiomyopathy delays disease onset |
|
| Relations |
| BioSample |
SAMN10819242 |
| SRA |
SRX5291433 |
