run_metadata: 40127
This data as json
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| 40127 | SRR2834940 | SRX1389533 | SRS1136848 | SRP065355 | PRJNA300314 | Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration | GSE74415 | Transcriptome Analysis | Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation. | pubmed:27355827 | 0dpa mRNA rep 1 | GSM1920161 | source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA | 0dpa mRNA rep 1 | Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. | caudal fin | Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. | Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. | Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. | tissue:caudal fin|dy post amputation:0|library type:mRNA | GSM1920161 | GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq | GSM1920161 | 1 | Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. | GEO Accession:GSM1920161 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP065355 | C6E48ANXX_s2_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s2_2_GSLv3-7_04_SL87417.fastq.gz | fastq fastq | 579950700.0 | 3866338.0 | GSM1920161 r2 | 0:75 1:75 | A:158309372;C:131242268;G:131179210;T:159026086;N:193764 | 75 | 75 | 158309372 | 131242268 | 131179210 | 159026086 | 193764 | SRX1389533 | SRS1136848 | SRA307553 | GEO | Molecular and Biomedical Sciences, University of Maine | 2 | 0.91483 | 0.91594 | 0.11629 | 0.1161 | 0.73697 | 0.7361 | 0.48411 | 0.48009 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2015-10-27 | Adult | Adult | Fin | Surface Structure |