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| Status |
Public on Nov 24, 2024 |
| Title |
Mussel gill tissues, long time period, deep-sea, 10 days, rep1 |
| Sample type |
SRA |
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| Source name |
Gill tissues
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| Organism |
Mytilus galloprovincialis |
| Characteristics |
tissue: Gill tissues
cell line: not collected
cell type: not collected
genotype: Wildtype
treatment: Cold seep in situ exposure, 10 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from gill tissues was extracted using TRIzol and sent to Novogene (Beijing, China) for sequencing. RNA integrity was assessed using the Fragment Analyzer 5400 (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
musselgilltissuseinsitucollectedfromcoldseepinlong-termreplicate1
LT-1
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| Data processing |
Raw reads were conducted quality control by fastp version 0.12.4 with default parameters.
de novo assembly of the reference transcriptome using Trinity version 2.13.260 with default parameters, except for both “--min_kmer_cov” and “--min_glue” of 3 options to remove the low abundance transcripts. These transcripts were then clustered to elimination redundancy using CD-HIT version 4.8.1 with sequence identity threshold of 0.9, resulting in the generation of the reference transcriptome, named unigenes.
The clean data were aligned to unigenes using bowtie version 1.3.171, abundance estimation was quantified by Salmon version 1.7.0, and the genes expression levels were measured in transcripts per million (TPM).
Assembly: de novo assembly ; unigenes.fasta
Supplementary files format and content: tab-delimied text files include Length, EffectiveLength, TPM, and NumReads for each gene of each Sample
Supplementary files format and content: tab-delimied text files include TPM values for each Sample
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| Submission date |
Apr 10, 2024 |
| Last update date |
Nov 25, 2024 |
| Contact name |
Luyang Sun |
| E-mail(s) |
[email protected]
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| Organization name |
Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences
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| Department |
Single-Cell Center
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| Street address |
Songling Road 189#
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| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266101 |
| Country |
China |
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| Platform ID |
GPL34373 |
| Series (1) |
| GSE263620 |
RNA-Seq of shallow-water mussel Mytilus galloprovincialis under in situ hydrostatic pressure exposure |
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| Relations |
| BioSample |
SAMN40911293 |
| SRA |
SRX24206214 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8195534_LT-1.quant.sf.gz |
3.4 Mb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
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