EML histone readers prevent seed development without fertilization
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA454261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7082750_1.fastq.gz | Fastqsanger.gz | |||
| SRR7082750_2.fastq.gz | Fastqsanger.gz | |||
| SRR7082751_1.fastq.gz | Fastqsanger.gz | |||
| SRR7082751_2.fastq.gz | Fastqsanger.gz | |||
| SRR7082752_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:EML1 and EML3 were previously shown to be histone readers involved in plant-pathogen interactions. To learn more about the developmental function of EML1 and EML3, we generated eml1 eml3 double mutant and showed that it had specific seed developmental phenotypes, including a capability to develop seed without fertilization. Next, we analyzed the mRNA expression of genes in the eml1 eml3 double mutant and compared it to its wild type. Differentially expressed (DE) genes in the mutant were identified and compared with DE of the mutants known to be involved in regulating seed development and in fertilization-independent endosperm development. Our results suggest that some targets are shared between EML histone readers and known regulators of seed development, such as MEA. Auxin response seems to be affected in both types of mutants. However, unlike MEA, EML proteins regulate auxin responsive genes not only in the endosperm, but also in the embryo. This capability makes EML proteins very good candidates for engineering apomictic seeds.
2019-05-01 | GSE113847 | GEO
Project description:To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes involved with some storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. Hundreds of transcription factors with notable expression in at least one stage of seed development were also identified and examined. Results from a second biological replicate demonstrate high reproducibility of these data.
2013-03-18 | GSE42871 | GEO
Project description:To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes involved with some storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. Hundreds of transcription factors with notable expression in at least one stage of seed development were also identified and examined. Results from a second biological replicate demonstrate high reproducibility of these data. High-throughput sequencing using Illumina Genome Analyzer II and Illumina HiSeq 2000 (RNA-Seq) was performed on seven stages of soybean seeds, with two biological replicates per stage.
2013-03-18 | E-GEOD-42871 | biostudies-arrayexpress
Project description:Enforced expression of the homeobox transcription factor HOXB4 has been shown to enhance hematopoietic stem cell (HSC) self-renewal and expansion ex vivo and in vivo. In order to investigate the largely unknown downstream targets of HOXB4 in hematopoietic progenitor cells, HOXB4 was constitutively overexpressed in the primitive hematopoietic progenitor cell line, EML. Gene expression differences were compared between KLS (c-Kit+, Lin-, Sca-1+)-EML cells that overexpressed HOXB4 (KLS-EML-HOXB4) to control KLS-EML cells that were transduced with vector alone. ChIP-chip was used to identify promoter regions bound by HOXB4.
2010-04-20 | GSE20604 | GEO
Project description:Enforced expression of the homeobox transcription factor HOXB4 has been shown to enhance hematopoietic stem cell (HSC) self-renewal and expansion ex vivo and in vivo. In order to investigate the largely unknown downstream targets of HOXB4 in hematopoietic progenitor cells, HOXB4 was constitutively overexpressed in the primitive hematopoietic progenitor cell line, EML. Gene expression differences were compared between KLS (c-Kit+, Lin-, Sca-1+)-EML cells that overexpressed HOXB4 (KLS-EML-HOXB4) to control KLS-EML cells that were transduced with vector alone. ChIP-chip was used to identify promoter regions bound by HOXB4. We overexpressed HOXB4 in EML cells. We isolated 3 separate single cell clones as assessed by Southern Blot Analysis (3 clones for EML-HOXB4 and 3 clones for control EML-GFP cells). RNA was isolated from the KLS (c-Kit+, Lin-, Sca-1+) fraction of each single cell clone population and processed for hybridization to array chips using established lab protocols. Chip-Chip analysis of the three HOXB4 overexpressing clones was performed to identify HOXB4 bound promoters.
2010-04-20 | E-GEOD-20604 | biostudies-arrayexpress
Project description:We report the application of sequencing technology for high-throughput profiling of RUNX1 transcription factor occupancy in mouse EML cells. RUNX1 antibody was use for chromatin immunoprecipitation followed by high-throughput sequencing to reveal RUNX1 genome occupancy in hematopoietic stem/progenitor cells. Examination of RUNX1 transcription factor occupancy in EML cells.
2014-10-24 | E-GEOD-62596 | biostudies-arrayexpress
Project description:Carbon (C) and nitrogen (N) contents of grain-filling stage are keys item that determined the growth of rice, and also the quality of seed. Therefore, to elucidating the mechanism of C/N signaling in a seed is an important problem for crops whose seed is used as food like rice. The DNA microarray analysis with the rice seed which was performed the additional fertilizer at the time of heading, in order to clarify how C/N signal change of the rhizosphere in seed production stage affects a seed component on a gene expression level. Fertilization was supplied at the same time of plantation and performed middle fertilizing 37 days after germination. 400 mg of ammonium chloride (NH4 Cl) was supplied at the time of heading to the “ + NH4 Cl ” group. Rice seeds were selected from 6 plants for RNA extraction, and hybridization on Affymetrix microarrays. We sought to understand the change of gene expression by the additional fertilization.
2014-08-04 | E-GEOD-49818 | biostudies-arrayexpress
Project description:Mucor koreanus EML-QT1 Genome sequencing and assembly
| PRJNA1106014 | ENA
Project description:We report the application of sequencing technology for high-throughput profiling of RUNX1 transcription factor occupancy in mouse EML cells. RUNX1 antibody was use for chromatin immunoprecipitation followed by high-throughput sequencing to reveal RUNX1 genome occupancy in hematopoietic stem/progenitor cells.
2014-10-24 | GSE62596 | GEO
Project description:Nocardia cyriacigeorgica strain:EML 446 Genome sequencing and assembly
| PRJNA542857 | ENA