Zebrafish metagenome
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ABSTRACT:
PROVIDER: PRJNA670812 | ENA |
REPOSITORIES: ENA
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Project description:Small RNA high-throughput sequencing technology was used to characterize the miRNAs in F1-zebrafish after 90-day β-diketone antibiotic (DKA) exposure to F0-zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7-dpf F1-zebrafish were constructed. In total, 10,117,347, 9,818,830 and 12,049,949 raw reads were acquired, respectively, under the different DKA-exposure treatments (0, 6.25 mg/L and 12.5mg/L) from the three miRNAs libraries by Illumina sequencing. Low-quality reads were removed, which included 5' contaminants, those missing the 3' primer or insert tag, sequences with a poly A tail, and those shorter than 17 nt and longer than 25 nt. As a result, 8,141,146 (representing 312,735 unique sequences; control), 8,687,210 (representing 251,508 unique sequences; 6.25 mg/L), and 10,569,566 (representing 441,938 unique sequences; 12.5 mg/L) valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar, and the unique sRNA reads were mainly distributed in the 20-24 nt range, among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads, respectively. The 22-nt sRNAs were the most abundant, with the length distribution of counts of sequ-seqs and unique miRNAs displaying a normal distribution.
2016-07-30 | GSE85004 | GEO
Project description:Small RNA high-throughput sequencing technology was used to characterize the miRNAs in F1-zebrafish after 90-day β-diketone antibiotic (DKA) exposure to F0-zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7-dpf F1-zebrafish were constructed. In total, 10,117,347, 9,818,830 and 12,049,949 raw reads were acquired, respectively, under the different DKA-exposure treatments (0, 6.25 mg/L and 12.5mg/L) from the three miRNAs libraries by Illumina sequencing. Low-quality reads were removed, which included 5' contaminants, those missing the 3' primer or insert tag, sequences with a poly A tail, and those shorter than 17 nt and longer than 25 nt. As a result, 8,141,146 (representing 312,735 unique sequences; control), 8,687,210 (representing 251,508 unique sequences; 6.25 mg/L), and 10,569,566 (representing 441,938 unique sequences; 12.5 mg/L) valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar, and the unique sRNA reads were mainly distributed in the 20-24 nt range, among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads, respectively. The 22-nt sRNAs were the most abundant, with the length distribution of counts of sequ-seqs and unique miRNAs displaying a normal distribution. Sample 1: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 12.5 mg/L.
2016-07-30 | E-GEOD-85004 | biostudies-arrayexpress
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2013-05-13 | E-ERAD-84 | biostudies-arrayexpress
Project description:zebrafish metagenome Genome sequencing and assembly
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Project description:MicroRNAs (miRNAs) are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development, but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here, we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA, rRNA, snRNA, snoRNA and miRNA. By mapping to the zebrafish genome, we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families, including zebrafish specific families, such as mir-731, mir-724, mir-725, mir-729 and mir-2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate.
2015-04-01 | GSE61984 | GEO