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| Status |
Public on Nov 20, 2023 |
| Title |
channel catfish mucus, 10.8-month, replicate 3 |
| Sample type |
SRA |
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| Source name |
mucus
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| Organism |
Ictalurus punctatus |
| Characteristics |
tissue: mucus
strain: Ictalurus punctatus x Ictalurus punctatus
age: 10.8 month
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA were extracted from muscle, liver, intestine, mucus, and heart of blue catfish and channel catfish with three replicates using Quick RNA Microprep Kit (Zymo Research, Irvine, CA, USA).
The library for each tissue sample was constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The raw reads quality was assessed by FastQC (version 0.11.6)
Low-quality bases and adapter sequences were trimmed using Trimmomatic (version 0.39)
RNA-seq reads were aligned to the blue catfish (Ictalurus furcatus) reference genome using STAR aligner version 2.7.5c
The gene read counts of each sample were quantified and summarized using HTseq version1.0 (Anders et al. 2015)
Assembly: GCA_023701845.2
Supplementary files format and content: tab-delimited text file includes gene read counts for each sample
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| Submission date |
Nov 15, 2023 |
| Last update date |
Nov 20, 2023 |
| Contact name |
Xu Wang |
| E-mail(s) |
xzw0070@auburn.edu
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| Organization name |
Auburn University
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| Department |
Pathobiology, College of Veterinary Medicine
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| Street address |
273 CASIC Building, Auburn Research Park, 559 Devall Dr
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| City |
Auburn University |
| State/province |
AL |
| ZIP/Postal code |
36849 |
| Country |
USA |
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| Platform ID |
GPL30901 |
| Series (1) |
| GSE247918 |
Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in tank culture environment |
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| Relations |
| BioSample |
SAMN38271127 |
| SRA |
SRX22540337 |
| 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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