Ontology highlight
ABSTRACT:
PROVIDER: PRJNA729120 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:NKD1, 2 and O2 are key transcription factors interactively regulating endosperm development. Their mutation combinations may diversely alter the global gene regulatory landscape. To investigate how interactions between NKD1, 2 and O2 affect endosperm regulatome, which is indicated by accessible regions for regulators on chromatins, Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed for 16 DAP endosperms of all 8 genotype combinations (2 biological replicate per genotype). Among 16 sequenced samples, 20,478 to 49,640 (mean: 34,766) peaks were called, and these peaks represent potential chromatin accessible regions. Distribution of the peaks on chromatins varies among samples: 54.35% - 66.73% peaks are located at distal intergenic region (>3kb upstream and >300 bp downstream of a gene) and 6.7% - 12.1% are located at promoter region (within 3 kb flanking transcription starting site), and 4.62% - 8.88% peaks are located within 1kb flanking transcription starting site. Also, in WT background, nkd1 and nkd2 single mutants have overall greater number of opening regions (upregulated peaks) than closing regions (downregulated peaks), whereas nkd1,2 double mutant has similar number of opening and closing regions. In contrast, in o2-background, all nkd1, nkd2 and nkd1,2 mutants have greater number of closing than opening regions. This indicates that o2 may alter differential accessibility of nkd1, nkd2 single or nkd1,2 double mutants.
2023-10-09 | GSE214415 | GEO
Project description:Investigation of gene expression level changes in snapdragon petals and sepals during flower development The flower developmental stages analyzed in this study are representative of distinct developmental events: (i) preanthesis, (ii) anthesis, (iii) maturation and (iv) presenescence and are further described in the accompanying article. A 24 chip study using total RNA recovered from samples of petal and sepal tissue of Antirrhinum majus cv. Maryland True Pink harvested at four different stages of flower development, namely (i) preanthesis (three days before flower opening=d-3), (ii) anthesis (day of flower opening=d1), (iii) maturation (four days after flower opening=d4) and (iv) presenescence (seven days after flower opening=d7). Three separate samples were extracted per tissue and developmental stages. Each chip measures the expression level of 11,959 ESTs from Antirrhinum majus cv. Maryland True Pink with up to six 60-mer probes per target.
2012-06-06 | E-GEOD-36356 | biostudies-arrayexpress
Project description:We performed open chromatin analysis and genome-wide analysis for RAR-DNA association, on the hiPSC-derived cells in the 2C protocol. The purposes were to analyze sequential opening and closing of chromatin elements, and to elucidate the molecular roles of RAR, in each differentiation stage of the 2C protocol.
2019-08-08 | GSE109172 | GEO
Project description:Chemical induction of pluripotency (CIP) is an ideal way to reprogram cell fate, but remains poorly understood. Here we report the development of an efficient CIP protocol and the chromatin accessibility dynamics (CAD) during CIP by ATAC-seq. CIP first reorganizes the somatic genome to an intermediate state that must be resolved by primarily closing loci opened earlier before reaching a pluripotent state with gradual opening of loci enriched with motifs for the OCT/SOX/KLF families. Bromodeoxyuridine, a critical ingredient of CIP, is responsible for both closing and opening critical loci, at least in part by preventing the opening of loci enriched with motifs for the AP1 family and facilitating the opening of loci enriched with SOX/KLF/GATA motifs. Our studies provide the first link between small molecules and nuclear architecture in the context of cell fate decisions.
2018-04-10 | GSE110262 | GEO
Project description:Chemical induction of pluripotency (CIP) is an ideal way to reprogram cell fate, but remains poorly understood. Here we report the development of an efficient CIP protocol and the chromatin accessibility dynamics (CAD) during CIP by ATAC-seq. CIP first reorganizes the somatic genome to an intermediate state that must be resolved by primarily closing loci opened earlier before reaching a pluripotent state with gradual opening of loci enriched with motifs for the OCT/SOX/KLF families. Bromodeoxyuridine, a critical ingredient of CIP, is responsible for both closing and opening critical loci, at least in part by preventing the opening of loci enriched with motifs for the AP1 family and facilitating the opening of loci enriched with SOX/KLF/GATA motifs. Our studies provide the first link between small molecules and nuclear architecture in the context of cell fate decisions.
2018-04-10 | GSE110261 | GEO
Project description:Water deficit stress (WDS) is a crucial factor that causes the inhibition of petal expansion and abnormal flower opening in rose. The regulatory mechanisms of petal expansion by WDS at transcriptional level were investigated by analysis expression profiles under WDS. Analysis used total RNA samples of petals taken from flowers treated by WDS comparison to those from control flowers. Transcriptome dynamics during treatment time responsive to WDS.
2013-01-09 | E-GEOD-33217 | biostudies-arrayexpress
Project description:n Arabidopsis thaliana, the non-pollinated floral stigma degenerates about 3 to 4 days after flower opening. This data set describes the changes in the stigma transcriptome profiles during this senescence process. Three timepoints cover the young (TP1), the mature (TP2), and the senescent (TP3) stigma.
2018-05-01 | E-MTAB-6279 | biostudies-arrayexpress
Project description:affy_petaldvt_lyon_rose. The objective is to identify genes involved in petal development in rose. We aim at identifying genes whose expression correlates with flower opening and scent emission. In this study, we used a microarray approach to compare the transcriptome of a scented rose flower (PF) versus non-scented rose flower (RF). Samples (petal tissues) were collected at the same time early in the afternoon. Total RNA was extracted using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays. Keywords: scented vs non-scented flowers 4 arrays - rose. Scented and non-scented flowers, 2 replicates each.
2011-08-31 | E-GEOD-18357 | biostudies-arrayexpress
Project description:affy_petaldvt_lyon_rose. The objective is to identify genes involved in petal development in rose. We aim at identifying genes whose expression correlates with flower opening and scent emission. In this study, we used a microarray approach to compare the transcriptome of a scented rose flower (PF) versus non-scented rose flower (RF). Samples (petal tissues) were collected at the same time early in the afternoon. Total RNA was extracted using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays. Keywords: scented vs non-scented flowers
2011-09-01 | GSE18357 | GEO