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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ENF1 (enlarged fil expression domain1) vs wild-type Col.

ABSTRACT: ENF1 gene (AT1G79440) encodes succinic semialdehyde dehydrogenase. Loss-of-function mutant of ENF1 shows pleiotropic phenotypes, including abnormal gene expression along the adaxial-abaxial axis in leaf development. enf1-1 allele has a point mutation in the splicing accepter site of 11th intron of ENF1. enf1-6 allele has T-DNA insertion in 5th exon of ENF1. Differential gene expression between in enf1 and in wild type was measured at shoot apex of six-day-after-sowing seedlings. Independent experiments for wild type, enf1-1, and enf1-6 were performed four, three, and three times, respectively.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Koichi Toyokura

PROVIDER: E-GEOD-24895 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ENF1 (enlarged fil expression domain1) vs wild-type Col.

Project description:ENF1 gene (AT1G79440) encodes succinic semialdehyde dehydrogenase. Loss-of-function mutant of ENF1 shows pleiotropic phenotypes, including abnormal gene expression along the adaxial-abaxial axis in leaf development. enf1-1 allele has a point mutation in the splicing accepter site of 11th intron of ENF1. enf1-6 allele has T-DNA insertion in 5th exon of ENF1.

2013-10-21 | GSE24895 | GEO

662107

Project description:Adaxial and Abaxial Leaf Metagenomes

| PRJNA591421 | ENA

CRABS CLAW positively regulates genes involved in the establishment of both abaxial and adaxial identity in Arabidopsis

Project description:CRABS CLAW (CRC) encodes a transcription factor of the plant-specific YABBY class in the model plant Arabidopsis thaliana. This gene is highly expressed in the abaxial (external) domain of the gynoecium wall and contributes to the establishment of abaxial-adaxial (external-internal) polarity in that tissue. Here we derive a list of putative target genes of CRC, which include AUXIN RESPONSE FACTOR4 (ARF4) and ASSYMETRIC LEAVES1 (AS1), both of which are known to be involved in the establishment of abaxial-adaxial polarity in lateral organs. ETTIN (ETT), which is partially redundant with ARF4, was not identified as a direct target of CRC, and this observation led us to predict that crc/ett double mutants might resemble ett/arf4 double mutants, which show a very strong breakdown of abaxial-adaxial polarity in the gynoecium wall. We have confirmed this prediction by constructing double mutants using several available mutant alleles of crc, ett and arf4. Interestingly, AS1 plays a role in the establishment of adaxial tissue identity in lateral organs, though its expression is not restricted to the adaxial domain. The observed positive regulation of AS1 by CRC may thus occur very early in gynoecium development, before CRC expression becomes polarised, or at later stages of development, specifically in the abaxial domain.

2021-03-05 | GSE14659 | GEO

Methylation Changes in Soybean Early Maturation Seed Compartments Using LCM

Project description:What methylation changes are occurring in different compartments of early maturation stage seed largely remains unknown. To uncover the possible role of DNA methylation in different compartments of early maturation stage seed, we characterized the methylome of two major compartments in embryonic cotyledon: cotyledon abaxial parenchyma (EM-COT-ABPY) and cotyledon adaxial parenchyma (EM-COT-ADPY) using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from cotyledon abaxial parenchyma (EM-COT-ABPY) and cotyledon adaxial parenchyma (EM-COT-ADPY) compartments.

2012-05-11 | E-GEOD-37893 | biostudies-arrayexpress

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii and piezosensible Pyrococcus furiosus

Project description:Pyrococcus yayanosii CH1 is the first and only obligate piezophilic hyperthermophilic microorganism discovered so far, that extends the physical and chemical limits of life on Earth and strengthens the idea of the existence of a hyperthermophilic biosphere in the depth of our planet. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses where performed in order to study the mechanisms implemented by the cell to face high hydrostatic pressure variations. In silico analyses showed that P. yayanosii genome is highly adapted to its harsh environment with precisely a loss of aromatic amino acid biosynthesis and the high constitutive expression of the energy metabolism compared to others non obligate piezophilic Pyrococus. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and CRISPR-cas. Cells were grown at different hydrostatic pressures (20, 52 and 80 Mpa for P. yayanosii and 0.1 and 45 Mpa for P. furiosus) until they reached the middle of the exponential phase. Each culture was done 3 times independantly.

2015-09-09 | E-GEOD-72783 | biostudies-arrayexpress

Single cell sequencing reveals phloem loading occurs via the abaxial bundle sheath cells in maize leaves [scRNA-seq]

Project description:Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c were also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in which abBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. The observations provide first insights into the unique properties of abBS cells, cells previously considered to fulfill the same functions as other bundle sheath cells (BSCs), and a basis for understanding the C4 syndrome.

2021-03-02 | GSE157757 | GEO

Single cell sequencing reveals phloem loading occurs via the abaxial bundle sheath cells in maize leaves [bulk RNA-seq]

2021-03-02 | GSE157758 | GEO

B. subtilis: temporal expression response to amino acid treatment

Project description:Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pool. In this study, an Agilent customized microarray representing approximately 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses. Amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to pulses of valine, glutamate, and glutamine, respectively, and Val-, Glu and Gln-specific genes were further distinguished from them. Different amino acid treatments were compared in terms of both the global temporal profiles and the 5-minute quick regulations, and between-experiment differential genes were identified. The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, hierarchical clustering and enrichment of functional categories. The results revealed the common and distinct modes of action of these three amino acids, and should help to elucidate the specific signaling mechanism of each amino acid as an effector. Three amino acids (Glutamate, Glutamine, and Valine) were adopted to perturb the culture of subtilis. Four time-points were investigated for each perturbation. There are two replicates for the first time-point of Valine-treatment experiment.

2010-05-05 | E-GEOD-17243 | biostudies-arrayexpress

Klebsiella pneumoniae: WT vs. Hfq mutant

Project description:Transcriptional profiling of K. pneumoniae comparing the wild type strain (S5) with a hfq deletion mutant (H0201). Goal was to determine the effects of Hfq absence on global K. pneumoniae gene expression. WT vs. Hfq mutant. Eight replicates for each ORF presented in the 44K array.

2013-01-11 | E-GEOD-29448 | biostudies-arrayexpress

Analysis of differentially expressed proteins （DEPs） in tomato leaves under the abaxial leafy supplemental lightning (AB) and the adaxial leafy supplemental lightning (AD)

Project description:Analysis of differentially expressed proteins （DEPs） in tomato leaves under the abaxial leafy supplemental lightning (AB) and the adaxial leafy supplemental lightning (AD)

2022-11-18 | PXD038211 | iProX

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