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| Status |
Public on Nov 28, 2021 |
| Title |
G 96h repeat2 |
| Sample type |
SRA |
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| Source name |
Gill
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| Organism |
Larimichthys crocea |
| Characteristics |
tissue: Gill
time point: 96h
agent: Cryptocaryon irritans
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen, USA), according to the manufacturer's instructions. Genomic DNA was removed using DNase (New England Biolabs), and RNA purity was assessed using the NanoDrop 2000 (NanoDrop Technologies, USA). The integrity of each RNA sample was detected by agarose gel electrophoresis and had an A260:A280 ratio and A260:A230 ratio. The RNA samples were used for the subsequent library construction.
standard illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
G 96h repeat2
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| Data processing |
TrimGalore (https://github.com/FelixKrueger/TrimGalore) and FastQC were used to control the quality of sequencing data.
The clean reads were aligned to a reference genome of L. crocea by Hisat2 (v. 4.8.5).
Samtools (v. 1.10) was used to filt out the mapping reads which were de-novo assembled separately for each sample by StringTie (v. 2.1.4).
the assembled transcriptomes of each sample were merged to an integrated transcriptome of all tissues by StringTie (v. 2.1.4) using “--merge” option.
Based on the Hisat2 alignment BAM file, StringTie and Deseq2 were used to estimate and quantify gene expression separately for each RNA-seq data with default parameters
Genome_build: GenBank: RQIN00000000.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
May 11, 2021 |
| Last update date |
Nov 28, 2021 |
| Contact name |
Yulin Bai |
| E-mail(s) |
[email protected]
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| Phone |
18616831168
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| Organization name |
Xiamen University
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| Street address |
Xiang'an South Road
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| City |
Xiamen |
| ZIP/Postal code |
361000 |
| Country |
China |
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| Platform ID |
GPL30112 |
| Series (1) |
| GSE174221 |
Comparative Transcriptome Analysis Reveals immunoregulation mechanism of lncRNA-mRNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection |
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| Relations |
| BioSample |
SAMN19105304 |
| SRA |
SRX10841850 |
| 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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