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Sample GSM6900588

Query DataSets for GSM6900588

Status

Public on Mar 26, 2023

Title

poePro_s40_embryo_lineB_n11

Sample type

SRA

Source name

embryo

Organism

Poeciliopsis prolifica

Characteristics

strain: line B
treatment: untreated
cultured time: uncultured

Extracted molecule

total RNA

Extraction protocol

Total RNA samples were extracted from the whole body of juvenile P. prolifica (n = 3 for line A and n = 3 for line B) using the RNeasy Mini Plus kit (Qiagen, Redwood City, CA, USA).
For juvenile fish wholebody samples, standard double-strand RNA-seq libraries were constructed using the Illumina TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) and the NEXTFLEX Rapid RNA-Seq Kit for Illumina Sequencing (PerkinElmer, Hopkinton, MA, USA). To obtain information on the direction of transcription, single-strand RNA-seq libraries were prepared using the NEXTFLEX Rapid Directional RNA-Seq Kit (PerkinElmer, Hopkinton, MA, USA) and TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocols. libraries were sequenced in a 2×100 bp Paired-End (PE) setting on an Illumina HiSeq2000 machine. To characterize expression genes in the embryonic stages, total RNA samples were also extracted from early embryos at developmental stage 45 of P. prolifica line A and line B, and mRNA-seq libraries were prepared using the TruSeq RNA Library Prep kit v2 (Illumina, San Diego, CA, USA). After size check on an Agilent TapeStation 4200 using the High-Sensitive D1000 Screen Tape (Agilent Technologies, Santa Clara, CA, USA), the libraries were sequenced using a 2×125 bp PE format on an Illumina HiSeq2500 Sequencer .

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

The quality of raw reads were controlled using FastQC.
Sequencing adapter sequences and low-quality bases were trimmed using Trimmomatic v0.36.
High-quality reads were mapped to the reference P. prolifica genome assembly by Tophat-2.1.1.
The raw RNA-seq counts for each gene were determined using BEDtools
Assembly: P. prolifica genome assembly (GenBank assembly accession JAPDDK000000000)
Supplementary files format and content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene in all samples

Submission date

Dec 28, 2022

Last update date

Mar 26, 2023

Contact name

Xu Wang

E-mail(s)

xzw0070@auburn.edu

Organization name

Auburn University

Department

Pathobiology, College of Veterinary Medicine