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Sample GSM2266457 Query DataSets for GSM2266457
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
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
BioSample SAMN05554696
SRA SRX2011204

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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