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| Status |
Public on Jan 01, 2024 |
| Title |
gut, 10 μg/L NIC exposure group, rep2 |
| Sample type |
SRA |
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| Source name |
gut
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| Organism |
Pelodiscus sinensis |
| Characteristics |
tissue: gut
genotype: WT
treatment: 10 μg/L NIC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
L_gut_2
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| Data processing |
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000.
Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Assembly: the reference genome of Pelodiscus sinensis (GenBank No. 309658)
Supplementary files format and content: tab-delimited txt file includes FPKM values for each sample
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| Submission date |
Feb 20, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Hao Wu |
| E-mail(s) |
wh17380133463@126.com
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| Phone |
+8617380133463
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| Organization name |
Hunan Fisheries Science Institute
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| Street address |
Shuanghe Road 728, Kaifu District, Changsha
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| City |
Changsha |
| ZIP/Postal code |
410153 |
| Country |
China |
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| Platform ID |
GPL33144 |
| Series (1) |
| GSE225631 |
Environmentally relevant concentrations of niclosamide disrupt antioxidant defense, histology, and the liver and intestine transcriptome of Chinese soft-shelled turtle |
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| Relations |
| BioSample |
SAMN33380752 |
| SRA |
SRX19443797 |
| 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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