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Status |
Public on Jun 27, 2023 |
Title |
C. virginica, 2'3'-cGAMP, 12h, rep 3 |
Sample type |
SRA |
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Source name |
Gill tissue
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Organism |
Crassostrea virginica |
Characteristics |
tissue: Gill tissue genotype: wild type treatment: 2'3'-cGAMP
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Extracted molecule |
total RNA |
Extraction protocol |
Gill tissues were preserved in RNAlater and total RNA extraction was performed by Novogene Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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Description |
Labeled as GA12_3 in processed data file, gene annotation listed in C_virginica_gene_annotation.xls, gene sequence listed in C_virginica_gene_sequence.fasta
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Data processing |
Sequencing reads were aligned to Crassostrea virginica C_virginica-3.0 reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_002022765.2/) using HISAT2 (Kim et al., 2019), and reads mapped to genes were summarized using featureCounts (Liao et al., 2014) by Novogene. Differentially expressed genes between each treatment and the control samples were next identified using DESeq2 (Love et al., 2014) (absolute log2 fold change > 1 and adjusted p value < 0.05). Assembly: Crassostrea virginica C_virginica-3.0 reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_002022765.2/) Supplementary files format and content: TSV file containing gene counts of each library
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Submission date |
May 09, 2023 |
Last update date |
Jun 27, 2023 |
Contact name |
Yao Li |
E-mail(s) |
yaoli0086@gmail.com
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Organization name |
Dana-Farber Cancer Institute
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Street address |
1 Jimmy Fund Way, SM512
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
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Platform ID |
GPL33398 |
Series (1) |
GSE232087 |
Effect of cyclic dinucleotides produced by cGAS-like receptors on gene expression in Crassostrea virginica |
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Relations |
BioSample |
SAMN35016269 |
SRA |
SRX20273779 |
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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