|
| Status |
Public on May 01, 2017 |
| Title |
adult_heart_0 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish adult heart
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: adult
tissue: heart
genotype: wild type
age: 6 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogenized using a mortar and pestle (Fisher Scientific), and total RNA was extracted using TRIzol (Sigma) according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument (Agilent Technologies) in the Mayo DNA sequencing core facility.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The flow cells were sequenced as 50×2 paired-end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software.
Raw RNA-seq reads were aligned to the zebrafish genome assembly (Zv9) for each sample using the Ensembl annotation Zv9 (Danio_rerio.Zv9.79.gtf) by TopHat (Version 2.0.12) . Each transcriptome was assembled by Cufflinks (Version 2.2.1) .
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) was calculated using a protocol from Cufflinks. Isoform_exp.diff was the result form Cuffdiff script, and isoforms.fpkm_table was the result from Cuffnorm script.
Genome_build: Zv9
|
| |
|
| Submission date |
Aug 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuji Zhang |
| E-mail(s) |
yuzhang@som.umaryland.edu
|
| Phone |
410-706-8523
|
| Organization name |
University of Maryland
|
| Street address |
660 W. Redwood Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE85416 |
Systematic identification and characterization of long non-coding RNAs in zebrafish through RNA-Seq |
|
| Relations |
| BioSample |
SAMN05554696 |
| SRA |
SRX2011204 |
