Gene Expression
Nebulas
Gene Expression NebulasSummary: We present an atlas of global gene expression as well as the evolutionary divergence covering embryo, endosperm and seed coat development in wheats and their diploid ancestors, providing insights into the evolution of gene expression in embryogenesis and grain development of wheat species.
Overall Design: We investigate the dynamics and evolution of gene expression throughout seven stages of embryo development (including the two cell, pre-embryo, transition, leaf early, leaf middle, leaf late and mature embryo), two stages of endosperm (transition stage endosperm and leaf late stage endosperm), and one pericarp stage (leaf early stage pericarp) across five wheat and ancestral grass species (AC -hexaploid, SF-tetraploid, DV-A genome diploid, SP-B genome diploid and TA-D genome diploid), two replicates for each stage.
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| Growth Protocol: | Polyploidy wheats, AC Barrie, Strong Field and diploid wheat grass (DV92) plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m-2 s-1 for whole life cycle. TA2780 and TA101132 were initially grown in a growth chamber at 22°C under long days (16h day/8h night), at the fifth-leaf stage, plants were moved into a cold room with 4°C and the long day photoperiod for one month (vernalization treatment), then move back to 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m-2 s-1 again to complete its life cycle |
| Treatment Protocol: | - |
| Extract Protocol: | Total RNA was extracted from embryo, endosperm and seed coat of wheat speciesat different development stages following the protocol of RNAqueous-Micro kit (Ambion, Catalog# 1927), two replicates for each development stage. |
| Library Construction Protocol: | The quantity of RNA isolated from early stage was insufficient for preparation of libraries for the RNA-seq experiments. Therefore the mRNA of all stages was amplified and the aRNA were used for RNA-seq analysis. The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750). For RNA-seq profile analysis, we prepared Illumina mRNA-seq libraries using the TruSeq RNA kit (version 1, rev A), the libraries were prepared by using aRNA according to manufacturer's instruction. For HiSeq 2500 sequencing, 4 libraries were pooled per sequencing lane Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf). |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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