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| Status |
Public on Dec 22, 2022 |
| Title |
skin, golden, rep2 miRNA |
| Sample type |
SRA |
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| Source name |
skin
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| Organism |
Carassius auratus |
| Characteristics |
tissue: skin
group: golden
Sex: female
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol (Invitrogen, UK)., and genomic DNA was removed using Dnase I (New England Biolabs), 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
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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 |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Carassius auratus (goldfish)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Sep 01, 2022 |
| Last update date |
Dec 22, 2022 |
| Contact name |
Mingkun Luo |
| E-mail(s) |
luomingkun@ffrc.cn
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| Organization name |
Nanjing Agricultural University
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| Department |
Wuxi Fisheries College
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| Street address |
East Shanshui Road 9
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| City |
Wuxi |
| State/province |
Jiangsu |
| ZIP/Postal code |
214081 |
| Country |
China |
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| Platform ID |
GPL32622 |
| Series (2) |
| GSE212497 |
Identification of miRNA information related to different skin color of golden-backed crucin carp |
| GSE212498 |
Identification of RNA information related to different skin color of golden-backed crucin carp |
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| Relations |
| BioSample |
SAMN30626167 |
| SRA |
SRX17663420 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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