Ontology highlight
ABSTRACT:
PROVIDER: PRJNA376191 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5282160.fastq.gz | Fastqsanger.gz | |||
| SRR5282180.fastq.gz | Fastqsanger.gz | |||
| SRR5282190.fastq.gz | Fastqsanger.gz | |||
| SRR5282200.fastq.gz | Fastqsanger.gz | |||
| SRR5282210.fastq.gz | Fastqsanger.gz |
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Project description:Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. The microarray included multiple probes for each of the ~32,500 stringently filtered genes identified in the B73 reference genome. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3,410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes that are present in B73 but missing from the genome of several other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes and the majority of events are observed in both maize and teosinte suggesting that these reflect relatively old variants that are not associated with domestication or maize improvement. Many of the genes affected by CNV/PAV are either maize-specific or members of genes families suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. Many plant genomes are relatively large and contain the remnant of whole genome duplications which may provide the ability to tolerate high levels of structural variation. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.
2010-10-15 | GSE23756 | GEO
Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures termed shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, marked by cell layering. Maize SAMs are comprised of two cell layers, L1 (single cell layered tunica) and L2 (corpus). To identify genes required for layer-specific functions intact maize SAMs were fixed, embedded in paraffin and sectioned. L1 and L2 cells were isolated from these sections via laser capture microdissection (LCM). RNA was isolated from six biological replications of L1 and L2, amplified and hybridized to microarrays spotted with ~37,000 maize cDNA clones. This experiment identified ~700 ESTs that are preferentially expressed in the L1 or the L2 (P <0.001). The L1-up-regulated ESTs included ZmOCL1 and ZmOCL4, which are known to exhibit L1-specific expression in the maize SAM. The L2-up-regulated ESTs included KNOTTED1, whose transcripts are known to accumulate in the L2 but not in the L1 of the maize SAM. Differentially expressed ESTs included genes involved in transcription, signal transduction, transport and metabolism, many of which are novel candidates that are required for layer-specific functions in the maize SAM. Several L1-up-regulated ESTs were annotated as yabby family genes or basic helix-loop-helix transcription factor-like genes, which have not previously been reported as having layer-specific expression in the SAM. Novel WW domain-containing genes (WW genes) were identified in this study. The WW domain mediates protein-protein interactions, often with signal transduction components. These WW genes were substantially up-regulated in the L1 relative to the L2. Keywords: Cell Type Comparison
2008-11-11 | GSE9610 | GEO
Project description:All above ground organs of higher plants are ultimately derived from shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, and monocot SAMs such as maize are comprised of two cell layers, a single cell layered tunica (L1) and a corpus (L2). Although recent research has revealed roles of these cell layers in the SAM, intra- and inter-cell-layer signaling networks involved in organ development remain largely unknown except for a few differentially expressed genes. Here, we used Illumnia technology to conduct RNA-seq of L1 and L2 cell layers in maize B73 maize shoot apical meristem.
2013-01-28 | GSE16868 | GEO
Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both SAMs (SAMs per se plus P0 and P1) and above-ground portions of seedlings collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have 14,400 informative spots from maize. Statistical analyses showed that approximately 6.3% and 6.5% of the tested genes were significantly (p <0.0001) up- and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were also up-regulated (p <0.01). The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kinds of enzymes, suggesting these genes play important roles in meristem maintenance and the early stage of leaf development in maize. Interestingly, several retrotransposon-related genes were greatly up-regulated in the SAM. This finding raised the possibility that retrotransposons are involved in regulatory mechanisms of maize SAM. Keywords: cell type comparison design
2007-11-13 | GSE4722 | GEO
Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both SAMs (SAMs per se plus P0 and P1) and above-ground portions of seedlings collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have over 37,000 informative spots from maize. Statistical analyses showed that approximately 7.4% and 6.0% of the tested genes were significantly (p <0.0001) up- and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were also up-regulated (p <0.01). The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kinds of enzymes, suggesting these genes play important roles in meristem maintenance and the early stage of leaf development in maize. Interestingly, several retrotransposon-related genes were greatly up-regulated in the SAM. This finding raised the possibility that retrotransposons are involved in regulatory mechanisms of maize SAM. Keywords: cell type comparison design
2007-06-07 | GSE6267 | GEO
Project description:The recessive mutation ragged seedling2-R (rgd2-R) conditions defective lateral development of maize leaves. Although dorsiventral patterning is established in rgd2-R mutant leaves, some swapping of adaxial/abaxial epidermal identity may occur. Molecular analyses indicate that RGD2 is required for the coordination of dorsiventral and lateral patterning during maize leaf development, yet the RGD2 gene product and the mechanisms of RGD2 function are unknown. In order to investigate the genetic mechanisms downstream of RGD2 gene function, SAM-specific transcriptional profiling of rgd2-R is compared to that of nonmutant using laser microdissection microarray. Whole SAMs were laser-microdissected from rgd2-R mutant and non-mutant seedlings grown under the same controlled conditions. Microarray profiles were generated for 28,671 maize cDNAs contained on gene chips SAM 1.1and SAM 3.0 (http://www.plantgenomics.iastate.edu/maizechip/). Keywords: Genetic modification
2008-05-03 | GSE11325 | GEO
Project description:Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. The microarray included multiple probes for each of the ~32,500 stringently filtered genes identified in the B73 reference genome. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3,410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes that are present in B73 but missing from the genome of several other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes and the majority of events are observed in both maize and teosinte suggesting that these reflect relatively old variants that are not associated with domestication or maize improvement. Many of the genes affected by CNV/PAV are either maize-specific or members of genes families suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. Many plant genomes are relatively large and contain the remnant of whole genome duplications which may provide the ability to tolerate high levels of structural variation. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation. 1-2 replications of 25 maize inbred and 14 teosinte genotypes were hybridized to an array designed from the ~32,400 genes in the maize B73 reference genome.
2010-10-15 | E-GEOD-23756 | biostudies-arrayexpress
Project description:Loss of function mutations in the narrow sheath (ns) duplicate genes (ns1 and ns2) cause the deletion of a mediolateral domain from maize leaves. The ns genes encode duplicate WUSCHEL1-like homeobox (WOX) putative transcription factors that function redundantly and non-cell autonomously to direct recruitment of leaf founder cell-initials in a lateral domain of the shoot apex. In order to investigate the genetic mechanisms of NS1 gene function, SAM-specific transcriptional profiling of narrow sheath mutant1-R comparing to that of nonmutant using laser microdissection microarray. Whole SAMs were laser-microdissected from ns1-R mutant and non-mutant seedlings grown under the same controlled conditions. Microarray profiles were generated for 37,662 maize cDNAs contained on gene chips SAM 1.1, SAM 2.0 and SAM 3.0 (For details, see the the Iowa State University Center for Plant Genomics website). Keywords: Genetic modification
2007-03-14 | GSE7248 | GEO
Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both SAMs (SAMs per se plus P0 and P1) and above-ground portions of seedlings collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have 14,400 informative spots from maize. Statistical analyses showed that approximately 6.3% and 6.5% of the tested genes were significantly (p <0.0001) up- and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were also up-regulated (p <0.01). The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kinds of enzymes, suggesting these genes play important roles in meristem maintenance and the early stage of leaf development in maize. Interestingly, several retrotransposon-related genes were greatly up-regulated in the SAM. This finding raised the possibility that retrotransposons are involved in regulatory mechanisms of maize SAM. An experimental aim is to identify genes preferentially expressed in maize SAM by comparing the transcript abundant between SAMs and seedlings using cDNA microarrays that have 14,400 informative spots from maize.
2010-06-25 | E-GEOD-4722 | biostudies-arrayexpress
Project description:Heritable variation in gene expression has been largely studied in model organisms by taking advantage of pure and inbred lines. Comparative studies on organisms with contrasting evolutionary history, population size and genome architecture have been hindered by practical considerations, as many of these species are poorly suited for breeding. We have developed a method for determining expression variation in an undomesticated tree species by directly measuring the segregation of gene expression in the haploid meiotic products of a single diploid individual. We show the utility of our approach by identifying expression variation that segregates consistent with one causal variant and identify an unexpectedly large number of these Mendelian expression traits. The megagametophyte approach opens the doors for the application of genetical genomics approaches in a large number of undomesticated plant species. Transcriptomics data from 18 megagametophytes of two unrelated mother trees. In tree 80112, all of the 18 megagametophytes were analyzed on to different microarrays with two different dyes. In tree 77111, 16 megagametophytes were replicated as above.
2012-11-30 | E-GEOD-35337 | biostudies-arrayexpress