|
| Status |
Public on Dec 25, 2022 |
| Title |
skin, golden, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Carassius auratus |
| Characteristics |
tissue: skin
group: gold
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
gold_1
|
| 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
|
| |
|
| Submission date |
Sep 01, 2022 |
| Last update date |
Dec 25, 2022 |
| Contact name |
Mingkun Luo |
| E-mail(s) |
luomingkun@ffrc.cn
|
| Organization name |
Nanjing Agricultural University
|
| Department |
Wuxi Fisheries College
|
| Street address |
East Shanshui Road 9
|
| City |
Wuxi |
| State/province |
Jiangsu |
| ZIP/Postal code |
214081 |
| Country |
China |
| |
|
| Platform ID |
GPL32622 |
| Series (2) |
| GSE212495 |
Identification of mRNA 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 |
|
| Relations |
| BioSample |
SAMN30626160 |
| SRA |
SRX17391527 |
