Glycine max
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA181945 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR618765.fastq.gz | Fastqsanger.gz | |||
| SRR618766.fastq.gz | Fastqsanger.gz | |||
| SRR618767.fastq.gz | Fastqsanger.gz | |||
| SRR618768.fastq.gz | Fastqsanger.gz |
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Project description:To understand the genetic mechanisms involved in the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue during soybean seedling development, we constructed seven different RNA-Seq libraries using cotyledons from each developmental stage separately. Analysis of RNA-Seq data from different developmental stages revealed the differential expression of many genes including transcription factors. In this study, we focused on NAC and YABBY transcription factors which showed a conspicuous expression pattern during soybean seedling development. Their expression gradually increases from stage 1 to stage 4 of soybean germinating cotyledons. The highest level of expression was found at stage 4. Then it gradually decreased as the germinating cotyledons develop a mature seedling. We investigated the differential expression of NAC and YABBY regulated genes between stage 3 (before the functional transition) and stage 6 (after the functional transition) using our RNA-Seq data. Based on our RNA-Seq data, we found that 10 genes are up-regulated and 21 genes are down-regulated by NAC transcription factor. Similarly we found that 19 genes are up-regulated and 27 genes are down-regulated by YABBY transcription factor. High-throughput sequencing using Illumina HiSeq 2000 (RNA-Seq) was performed on seven developmental stages of soybean seedlings, with two biological replicates per stage.
2014-07-29 | E-GEOD-42550 | biostudies-arrayexpress
Project description:To understand the genetic mechanisms involved in the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue during soybean seedling development, we constructed seven different RNA-Seq libraries using cotyledons from each developmental stage separately. Analysis of RNA-Seq data from different developmental stages revealed the differential expression of many genes including transcription factors. In this study, we focused on NAC and YABBY transcription factors which showed a conspicuous expression pattern during soybean seedling development. Their expression gradually increases from stage 1 to stage 4 of soybean germinating cotyledons. The highest level of expression was found at stage 4. Then it gradually decreased as the germinating cotyledons develop a mature seedling. We investigated the differential expression of NAC and YABBY regulated genes between stage 3 (before the functional transition) and stage 6 (after the functional transition) using our RNA-Seq data. Based on our RNA-Seq data, we found that 10 genes are up-regulated and 21 genes are down-regulated by NAC transcription factor. Similarly we found that 19 genes are up-regulated and 27 genes are down-regulated by YABBY transcription factor.
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Project description:Seedling Shoot RNA-Seq of 622 soybean accessions
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Project description:In order to dissect the gene regulatory network during the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue, we constructed ChIP-Seq libraries for NAC and YABBY transcription factors using pooled cotyledons from seedling developmental stage 4 and stage 5. Millions of raw reads obtained from ChIP-Seq libraries were aligned to the reference soybean genome using the ultrafast Bowtie aligner to obtain quantitative data for genome matched reads. MACS software was used to call peaks representing enriched binding sites for NAC and YABBY transcription factors. Based on our ChIP-Seq data, we identified 72 genes are potentially regulated by NAC transcription factor and 96 genes by YABBY transcription factor. The motif analysis using MEME discovered three separate motifs for the NAC and YABBY transcription factors. For the NAC transcription factor, three commonly found motifs were G[AT]G[AG]G[AG]GA, C[AC]C[GA][TC][GA]CC and TGGGCC . The first one matched to a known zinc finger motif and the last two were identified as leucine zippers in the database of plant transcription factor binding motifs, JASPAR CORE plants. Similarly the three most commonly found motifs for YABBY transcription factors are CC [CA][TC]C[TA][CT]C, GA[AG]AGAAA and CCCCAC . The first two motifs matched to a known zinc finger motif and the last one was an AP2 MBD-like motif. Construction of ChIP-Seq libraries for NAC and YABBY transcription factors using germinating cotyledons from seedling developmental stages
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