Smarce1-Differential & enrichment analysis
Description
This is an excel table that includes data of differential expression, Gene Ontology analysis and KEGG analysis. These data was generated from the comparison of mRNA sequences obtained from wild-type and smarce1 mutant dissected retinas. The smarce1 gene encodes a subunit of the BAF chromatin remodeling complex. We introduced loss-of-function mutations in this gene and characterized the eye phenotype. The excel document contains complete lists of the genes with significant differential expression, the GO groups encompassing these genes, and the gene pathways that are significantly represented according to the KEGGS protocol.
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Steps to reproduce
Pools of 60 dissociated eyes from 5dpf larvae (WT and Smarce1-/-) of three independent crosses were used for RNA extraction (Zymo Research). Each RNA sample was analyzed for quantity and purity with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Libraries and RNA sequencing and data analysis were conducted under contract by Novogene Co., Ltd according to their protocols, sequencing libraries were generated NEBNext®Ultra™RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturers’ recommendations and index codes were added to attribute sequences to each sample. Library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated. Raw reads were filtered and aligned with reference genes. The alignment data was utilized to calculate the distribution of reads on reference genes and the mapping ratio. The fragments per kilobase of transcript per million mapped reads (FPKM) method was used to calculate the expression levels. Differential expression analysis between two groups (≥three biological replicates per condition) was performed using the DESeq2 R package (1.14.1). The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Gene Ontology (GO) enrichment analysis of differentially expressed genes was determined with the clusterProfiler R package. GO terms with a P-value less than 0.05 were considered significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment was performed for the analysis of gene functions to obtain information on the cellular process of differentially expressed genes.
Institutions
- Universidad Nacional Autonoma de MexicoDistrito Federal, Coyoacan