Ena-DATASET-DCPTCUHK-05-09-2018-10:57:11:145-394 - samples
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PROVIDER: EGAD00001004324 | EGA |
REPOSITORIES: EGA
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Project description:Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts
| EGAD00001001609 | EGA
Project description:Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma
| EGAD00001000395 | EGA
Project description:RNA sequencing of maternal plasma
| PRJNA716199 | ENA
Project description:These experiments measure genome-wide RNA Pol II binding in precisely staged wild-type embryos at five time points spanning the maternal to zygotic transition (nuclear cycles 12 through 14) of Drosophila melanogaster. In addition, RNA Pol II binding at nuclear cycle 13 is measured in embryos mutant for either mei-41/ATR or zelda. To correlate RNA Pol II binding with replication stress, genome-wide profiles of Replication protein A (70kDa subunit, RpA-70 EGFP) were generated in parallel with RNA Pol II for both wild-type and zelda at nuclear cycle 13.
2015-03-05 | GSE62925 | GEO
Project description:The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. TSS selection grammars include a genome-wide shift during spermatogenesis to promoters with a novel, position-specific, core promoter element, present in >70% of male-specific promoters. Differential promoter usage in spermatogenesis includes the activation of cryptic internal promoters within polycistronic operons, alternative TSS selection within promoters of genes expressed in earlier development and the exclusion of trans-splice sites. In contrast, maternal promoters, which are active in endocycling nurse nuclei in O. dioica, lack position-specific motifs, have dispersed TSS usage, ordered nucleosomes around the TSS and typical histone modifications associated with broad promoters. Furthermore, our results indicate that the cell cycle regulator, E2F1, acts as a master regulator of these maternally expressed genes. Zygotic promoters are also predominantly broad and the vertebrate maternal to zygotic switch in mode of TSS-selection is absent. DNA methylation in gene bodies is an ancient property of eukaryotic genomes and is thought to repress alternative TSSs. We report a strong association between gene body DNA methylation, H3K4me3-depletion and TATA-dependent sharp promoters in O. dioica. Core promoter features may therefore determine the subset of gene bodies that are methylated in this invertebrate genome.
2018-02-05 | GSE78794 | GEO
Project description:Fetal spleens were collected at days 82 and 97 of gestation following maternal infection with BVDV on day 75 of gestation. A microarray was performed on RNA -> cDNA of the splenic samples. Treatment groups consist of Controls (non-infected) and PI (persistently infected).
2020-08-25 | GSE148323 | GEO
Project description:These experiments measure genome-wide RNA Pol II binding in precisely staged wild-type embryos at five time points spanning the maternal to zygotic transition (nuclear cycles 12 through 14) of Drosophila melanogaster. In addition, RNA Pol II binding at nuclear cycle 13 is measured in embryos mutant for either mei-41/ATR or zelda. To correlate RNA Pol II binding with replication stress, genome-wide profiles of Replication protein A (70kDa subunit, RpA-70 EGFP) were generated in parallel with RNA Pol II for both wild-type and zelda at nuclear cycle 13. Two replicates each for 5 time points for wild type RNA Pol II. Two replicates for mei-41 RNA Pol II, nuclear cycle 13. Two replicates for zelda RNA Pol II, nuclear cycle 13. Two replicates each for Rpa70-EGFP in wild-type or zelda, nuclear cycle 13, matched to the corresponding RNA Pol II sample.
2015-03-05 | E-GEOD-62925 | biostudies-arrayexpress
Project description:Previously, we discovered that the global regulator Hha is related to cell death in biofilms and regulates cryptic prophage genes. Here we show Hha induces excision of prophage CP4-57 and DLP12 by inducing excision genes and by reducing SsrA synthesis. SsrA is a tmRNA important for rescuing stalled ribosomes, contains an attachment site for CP4-57, and is shown here to be required for CP4-57 excision. These prophages impact biofilm development as deletion of 35 genes individually of prophage CP4-57 and DLP12 increase biofilm formation up to 17-fold, and 5 genes decrease biofilm formation up to 6-fold. In addition, CP4-57 excises during early biofilm development but not in planktonic cells, whereas DLP12 excision was detected at all the developmental stages for both biofilm and planktonic cells. CP4-57 excision leads to a chromosome region devoid of the prophage and formation of a phage circle (which is lost). These results were corroborated by a whole-transcriptome analysis that showed that complete loss of CP4-57 activated expression of the flg, flh, and fli motility operons and repressed expression of key enzymes in the tricarboxylic acid cycle and enzymes for lactate utilization. Prophage excision also results in the expression of cell lysis genes that reduce cell viability (e.g., alpA, intA, and intD). Hence, defective prophage are involved in host physiology via Hha and in biofilm formation by generating a diversified population with specialized functions in terms of motility and nutrient metabolism.
2009-04-27 | GSE14472 | GEO
Project description:To better characterize group IE like human breast cancer based on the gene profiles of estrogen actions through estrogen receptor alpha (ER alpha), we identified an ER alpha transcriptional regulatory network for cell cycle in silico. We used two datasets from cell line (Data 1) and clinical samples (Data 2), respectively. Analyses on Data 1 via trajectory clustering and Pathway-Express confirmed the significant estrogen effect on up-regulating cell cycle activities. The gene expression relationships between ER alpha and cell cycle genes were re-identified in Data 2 by three statistical methods – Galton-Pearson’s correlation coefficient, Student’s t-test and the coefficient of intrinsic dependence. They were mostly (56.09%)(46/82) re-confirmed by literature search. E2F1 was found to be the major ER alpha target in regulating cell cycle gene expressions (83.72%)(36/43) via suppressive mode. However, enhanced cell cycle progression via up-regulating some cell cycle genes was predicted in silico possibly involving E2F2, in part. Both tumorigenic and tumor suppressing activities indicated by this network were predicted. This network clearly provides a robust way for uncovering estrogen actions in an ER(+) subtype specific manner. Experiment Overall Design: Two clinical datasets were used in this study. One, the 37 clinical arrays (abbreviated as 37A) consist of 26 A for patients positive in estrogen receptor alpha (ER) and in progesterone receptor (PR) immunohistochemical stain (IHC) and 11A for patients negative in ER IHC. This dataset was designated as Data 2. The 31 clinical arrays (31A) consist of 20A for patients positive in ER status but negative in PR status and 11A which are the same as in 37A. This dataset was used for data comparison. All the signals from the mRNA profile of each sample in the experiments were normalized using the internal control RNA- Stratagene's human common reference RNA via statistical method 'rank consistant lowess. Finally, those ratios were transformed by Log2.
2009-08-14 | E-GEOD-17040 | biostudies-arrayexpress
Project description:We report the m6A methylation maps of zebrafish embryos during early development, and transcriptome-wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A-dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT, highlighting the critical role of the m6A mRNA methylation in animal development.
2017-02-07 | GSE79213 | GEO