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| Status |
Public on Jul 01, 2014 |
| Title |
Fbrain |
| Sample type |
SRA |
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| Source name |
breeding marine medaka
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| Organism |
Oryzias melastigma |
| Characteristics |
gender: female
tissue: brain
molecule subtype: size-selected RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from pooled tissue samples was extracted using the mirVanaTM miRNA isolation kit (Applied Biosystems) and treated with DNase (Ambion) to remove contaminating genomic DNA.
The total RNA libraries were constructed from brain, liver, ovaries from female and brain, liver, testis from male, with each prepared from 1 µg of total RNA. Small RNAs were gel purified for enrichment to under 30 nt in length, and Illumina adaptors (Integrated DNA technology) were ligated to their 5’ and 3’ ends to construct strand-specific cDNA libraries. The ligation products were used as a template for cDNA synthesis using SuperScript II Reverse Transcriptase (Invitrogen) and an oligonucleotide primer with sequence complementary to 3’ adapter was used to initiate cDNA synthesis. The cDNA was amplified by 12 cycles using AccuPrime™ Pfx DNA Polymerase (Life Technologies) and purified on Novex 8% TBE polyacrylamide gel (Invitrogen). Amplified DNA of 140-190 nt was extracted from the gel and purified using the QiaQuick Gel Extraction Kit (Qiagen).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
FB
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| Data processing |
Basecalls performed using RTA 1.9 and CASAVA 1.7.0.
The sequence reads were trimmed and removed for adaptor sequences and the expression values.
The filtered sequence reads were mapped with miRBase v17 using NCBI BLAST v2.2.19.
The abundance for miRNAs were calculated by reads per miRNA per million sequenced reads.
Genome_build: miRBase v17
Supplementary_files_format_and_content: tab-delimited text files include miRNA sequences, lengths and abundances.
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| Submission date |
Dec 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yunjuan Bao |
| Organization name |
University of Notre Dame
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| Street address |
1234 Notre Dame Avenue
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| City |
Notre Dame |
| State/province |
Indiana |
| ZIP/Postal code |
46556 |
| Country |
USA |
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| Platform ID |
GPL16350 |
| Series (1) |
| GSE42696 |
Identification and expression profiling of microRNAs in brain, liver and gonads of marine medaka (Oryzias melastigma) by Illumina small RNA Sequencing |
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| Relations |
| SRA |
SRX208117 |
| BioSample |
SAMN01822149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1048082_Fbrain_processed.txt.gz |
10.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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