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Sample GSM7311882

Query DataSets for GSM7311882

Status

Public on Jun 27, 2023

Title

C. virginica, control, 6h, rep 2

Sample type

SRA

Source name

Gill tissue

Organism

Crassostrea virginica

Characteristics

tissue: Gill tissue
genotype: wild type
treatment: control

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.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 3000

Description

Labeled as SC6_2 in processed data file, gene annotation listed in C_virginica_gene_annotation.xls, gene sequence listed in C_virginica_gene_sequence.fasta

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

Submission date

May 09, 2023

Last update date

Jun 27, 2023

Contact name

Yao Li

E-mail(s)

yaoli0086@gmail.com

Organization name

Dana-Farber Cancer Institute

Street address

1 Jimmy Fund Way, SM512