run_metadata: 39937
This data as json
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| 39937 | SRR2532445 | SRX1293418 | SRS1094785 | SRP064261 | PRJNA297221 | Heart Chamber Evolution Reveals Roles of Gene/Genome Duplications on Continuous Character Evolution in Vertebrates | GSE73522 | Other | We sequenced at mRNA level in adult hearts of zebrafish pamprey and sea squirt. Combined with other 11 vertebrate heart RNA Seq data online we conducted comprehensive evolutionary genomic analyses to address the contribution of gene/genome duplications on heart structure evolution. We observed that number of duplicate genes expressed in heart increased gradually with the increase of heart chamber number along the vertebrate phylogeny despite that most of them were duplicated at the time near to the origin of vertebrates or more ancient. Our research provides a clear cut example to show the relationship among gene duplication continuous character evolution like heart structure evolution and nature selection. Overall design: Examination of mRNA levels in thirteen vertebrate samples with different cardiac chamber number and one invertebrate sea squirt. | DRE mix 02 | GSM1897224 | source name:Heart|tissue:Heart | DRE mix 02 | The libraries were sequenced as paired end 100 bases using the HiSeq2000 Illumina Casava1.7 software used for basecalling. FastQC v0.10.1 was used to assess the quality of reads.then the raw reads were processed by using the FastX Toolkit v0.0.13. All processed reads were aligned to reference genome using TopHat v2.0.10 Kim et al. 2013 and bowtie2 v2.1.0 Langmead and Salzberg 2012 The unique mapped reads were assembled and the expression level of a gene were calculated as FPKM Fragments Per Kilobase of transcript per Million mapped reads using cufflinks v2.1.1 Trapnell et al. 2010 Genome build: KH Genome build: Pmarinus7.0 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample | Heart | All dissected heart tissues were stored in RNAlater Ambion before processing. Total RNA was extracted using the Trizol Invitrogen. following the manufacturer’s protocol. RNA quality was monitored using Narodrop 2000. The cDNA libraries were constructed according to the standard Illumina protocols. | tissue:Heart | GSM1897224 | GSM1897224: DRE mix 02; Danio rerio; RNA Seq | GSM1897224 | 1 | All dissected heart tissues were stored in RNAlater Ambion before processing. Total RNA was extracted using the Trizol Invitrogen. following the manufacturer’s protocol. RNA quality was monitored using Narodrop 2000. The cDNA libraries were constructed according to the standard Illumina protocols. | GEO Accession:GSM1897224 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP064261 | XIN_R1_001.fastq.bz2 XIN_R2_001.fastq.bz2 | fastq fastq | 3846233924.0 | 19040762.0 | GSM1897224 r1 | 0:101 1:101 | A:1013374196;C:876654183;G:885048319;T:1029455120;N:41702106 | 101 | 101 | 1013374196 | 876654183 | 885048319 | 1029455120 | 41702106 | SRX1293418 | SRS1094785 | SRA301217 | GEO | School of life science, Fudan univeristy | 2 | 0.92587 | 0.93169 | 0.13736 | 0.13738 | 0.77697 | 0.77404 | 0.53305 | 0.5358 | 101 | 101 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2015-09-28 | Undetermined | Undetermined | Heart | Cardiovascular System |