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Sample GSM3721287

Query DataSets for GSM3721287

Status

Public on Mar 01, 2020

Title

16cell_B

Sample type

SRA

Source name

embryos

Organism

Capra hircus

Characteristics

tissue: embryos

Extracted molecule

total RNA

Extraction protocol

Not provided

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the goat genome (Capra hircus – ARS1) by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference. Genes with FPKM > 0.1 in at least one sample were kept in downstream analysis for Pearson correlation, Principle Component Analysis (PCA) and cluster analysis using R. Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05 and fold change > 2. IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively.
Identification of stage-specific genes was performed as previously described 5 and expression pattern clusters were generated by the unsupervised hierarchical clustering analysis using R.
Genome_build: Capra hircus – ARS1
Supplementary_files_format_and_content: FASTQ

Submission date

Apr 12, 2019

Last update date

Mar 01, 2020

Contact name

Zongliang Jiang

E-mail(s)

z.jiang1@ufl.edu

Organization name

University of Florida

Department

Animal Sciences