run_metadata: 41260
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41260 | SRR4017368 | SRX2011202 | SRS1608488 | SRP081209 | PRJNA338400 | Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq | GSE85416 | Transcriptome Analysis | We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf adult heart of 6 mpf WIK fish and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart adult heart and adult muscle tissues | pubmed:28455512 | embryonic heart 2 | GSM2266455 | source name:zebrafish embryonic heart|developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days | embryonic heart 2 | 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 | zebrafish embryonic heart | 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 | developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days | GSM2266455 | GSM2266455: embryonic heart 2; Danio rerio; RNA Seq | GSM2266455 | 1 | 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 | GEO Accession:GSM2266455 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP081209 | 4dpf_embryonic_heart-3.FCD29WDACXX_L7_ICGATGT.bam.R1.fastq.gz 4dpf_embryonic_heart-3.FCD29WDACXX_L7_ICGATGT.bam.R2.fastq.gz | fastq fastq | 3994817760.0 | 39164880.0 | GSM2266455 r1 | 0:51 1:51 | A:984074495;C:1022214385;G:1003461979;T:984987096;N:79805 | 51 | 51 | 984074495 | 1022214385 | 1003461979 | 984987096 | 79805 | SRX2011202 | SRS1608488 | SRA451066 | GEO | University of Maryland | 2 | 0.93632 | 0.93575 | 0.12674 | 0.1252 | 0.75595 | 0.75649 | 0.53521 | 0.50945 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-08-10 | Larval | Larval | Heart | Cardiovascular System |