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| Status |
Public on Aug 11, 2017 |
| Title |
1DB-3 |
| Sample type |
SRA |
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| Source name |
1DB rep3
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| Organism |
Anas platyrhynchos |
| Characteristics |
developmental stage: 1 day of age
tissue: skin
breed: Pekin Duck
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the tissue using a mirVana miRNA Isolation Kit (Ambion, USA). The purified RNA yield was determined by the absorbance at 260 nm with an ND-2000 NanoDrop spectrophotometer (Thermo Fisher, USA), and RNA quality was evaluated with a BioAnalyzer 2100 system (Agilent Technologies, USA).
RNA smaller than 200 base pairs (bp) was enriched with the mirVana miRNA isolation kit (Ambion). The RNA was then precipitated with ethanol and dissolved in water. Small RNAs had linkers ligated to them and bar-coded cDNAs were prepared using a TruSeq Small RNA Sample Prep Kit (Illumina, USA) following the manufacturer’s instructions.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The small RNA sequence reads were pre-processed using FASTXToolkit (fastx_toolkit-0.0.13.2; http://hannonlab.cshl.edu/fastx_toolkit/commandline.html), excluding low-quality reads (ambiguous N, quality < 10 nt, and length <18 nt) as well as 3′ adapter, 5′adapter and poly(A) sequences.
Further annotation analyses were performed using the commercial software CLC Genomic Workbench 5.5.
Briefly, the resulting clean reads were aligned against various databases, including ncRNA, piRNA, and Rfam, allowing a maximum mismatch of 2 nt to remove noncoding RNA, such as rRNA, tRNA, snRNA, and snoRNA.The remaining sequences were analyzed by BLAST Gallus gallus search against Sanger miRBase (version 21.0).
Reads that did not match any database above were marked as non-annotation. Non-annotated sequences were searched against the Gallus gallus genome using the miRCat program included in the sRNAToolkit (http://srna-workbench.cmp.uea.ac.uk/tools/analysis-tools/mircat/). Using default settings, 100 nucleotides of genomic sequence flanking each side of the sequences were extracted for RNA secondary structure prediction using RNAfold [1]. Only with tipical stem-loop hairpins and the free energy lower than -20 kcal/mol could be considered to be potential novel miRNAs.
Normalize the expression of miRNA in eighteen libraries to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads×1000000.
Genome_build: Gallus gallus
Supplementary_files_format_and_content: miRNA reads count
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| Submission date |
Jul 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
xing yong chen |
| E-mail(s) |
xingyong_chen@sohu.com
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| Organization name |
Anhui Agricultural University
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| Department |
School Of Animal Science And Technology
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| Street address |
130 West Changjiang Road
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| City |
hefei |
| State/province |
anhui |
| ZIP/Postal code |
230036 |
| Country |
China |
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| Platform ID |
GPL22591 |
| Series (1) |
| GSE101542 |
Integrative Analysis of the Pekin Duck (Anas anas) MicroRNAome during Feather Follicle Development |
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| Relations |
| BioSample |
SAMN07358586 |
| SRA |
SRX3010381 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2705928_1d-3.txt.gz |
2.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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