Computational protocol: Oocyte-expressed yes-associated protein is a key activator of the early zygotic genome in mouse

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Protocol publication

[…] GV oocytes and four-cell embryos were collected from WT and Yap1fl/fl;Gdf9-Cre mice (100 oocytes or embryos per sample). Total RNA was extracted from the samples using the RNeasy Plus Micro kit (Qiagen) following the manufacturer's protocol. Before RNA isolation, 2 × 106 mRNA-RFP was added to calculate mRNA copy number in each sample. Extracted total RNA was used to build a sequencing library using the NEB Next Ultra RNA Library Prep Kit for Illumina. We sequenced the library by Illumina Hiseq 2500 and aligned RNA-seq reads to Mus musculus UCSC mm9 references with the Tophat software (http://tophat.cbcb.umd.edu/), and calculated the FPKM of each gene using Cufflinks (http://cufflinks.cbcb.umd.edu). The amount of total mRNA was calculated based on the FPKM of exogenous RFP. GO analysis for enrichment of genes was determined using the Database for Annotation, Visualization and Integrated Discovery. The RNA-seq data have been deposited in Gene Expression Omnibus under the accession number GSE74344. […]

Pipeline specifications

Software tools TopHat, Cufflinks
Databases GEO
Application RNA-seq analysis
Organisms Mus musculus, Homo sapiens