Comment[ArrayExpressAccession] E-GEOD-51069 MAGE-TAB Version 1.1 Public Release Date 2014-03-20 Investigation Title The 3M-bM-^@M-2-tag digital gene expression library construction and Illumina sequencing analysis of Wild Type and SPL-/- ovules with placenta Transcriptomes Comment[Submitted Name] The 3M-bM-^@M-2-tag digital gene expression library construction and Illumina sequencing analysis of Wild Type and SPL-/- ovules with placenta Transcriptomes Experiment Description To elucidate the molecular basis underlying early female reproductive development, Here, we used high-throughput tag-sequencing analysis to identify genes preferentially expressed in female meiocytes (FMs) by comparing gene expression profiles from wild type ovules undergoing megasporogenesis with those from the lacking megasporogenesis spl mutant ovules. A total of 862 genes were identified as FMs with levels that are consistently reduced in spl ovules in two biological replicates. Genes involved in biogenesis, metabolism, transporter activity and DNA binding were over-represented in female meiocytes, suggesting that female meiocytes are synthetically and metabolically more active. Total mRNA profiles of stage 10-11 old M-oM-,M-^Boral buds wild type (WT) and SPL-/- ovules with placenta were generated by deep sequencing, Repeat twice, using Illumina adaptor 2 (GEX adapter 2). Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name zhao Zhao Qin Person First Name lihua Lihua Yuan Person Email zhaolihua1017@163.com Person Affiliation Shanghai Institutes for Biological Sciences, CAS Person Phone +86-021-54924312 Person Address Shanghai Institutes for Biological Sciences, CAS, FengLin road 300#, shang hai, shang hai, China Person Roles submitter Protocol Name P-GSE51069-3 P-GSE51069-2 P-GSE51069-1 Protocol Description Illumina Casava1.7 software used for basecalling. Raw sequences were transformed into Clean Tags by filtering off empty reads, low-quality tags (containing ambiguous bases), adaptor-only tags, and tags that occurred only once (probably result from sequencing error). The remaining high quality sequences were mapped to the Arabidopsis thaliana genome (TAIR10, ftp://ftp.arabidopsis.org/Genes/TAIR10_genome_release). For conservative and precise annotation, sequences with perfect homology or only 1-nt mismatch were considered further. Clean tags aligned to multiple transcripts were excluded from our analysis. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and normalized to TPM (number of transcripts per million clean tags). When multiple types of tags were mapped to the different positions of the same gene, the gene expression levels were represented by the sum of all hit numbers Genome_build: The remaining high quality sequences were mapped to the Arabidopsis thaliana genome (TAIR10, ftp://ftp.arabidopsis.org/Genes/TAIR10_genome_release) Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample M-bM-^@M-& Dissected Ovule primordia from the ovaries were collected and stored in Qiagen RNAlater RNA stabilization reagent at 4M-0C,Total RNA was extracted from the ovule primordia with placenta tissues using the Qiagen RNAeasy Plant Mini kit.6M-NM-