# _embedded.samples[].characteristics.submission description[].text
In plants, reactive oxygen species and, more particularly, hydrogen peroxide (H2O2) play a dual role as toxic by-products of normal cell metabolism and as regulatory molecules in stress perception and signal transduction. Peroxisomal catalases are an important sink for photorespiratory H2O2. Using ATH1 Affymetrix microarrays, expression profiles were compared between control and catalase-deficient Arabidopsis (Arabidopsis thaliana) plants. Reduced catalase levels already provoked differences in nuclear gene expression under ambient growth conditions, and these effects were amplified by high light exposure in a sun simulator for 3 and 8 h. This genome-wide expression analysis allowed us to reveal the expression characteristics of complete pathways and functional categories during H2O2 stress. In total, 349 transcripts were significantly up-regulated by high light in catalase-deficient plants and 88 were down-regulated. From this data set, H2O2 was inferred to play a key role in the transcriptional up-regulation of small heat shock proteins during high light stress. In addition, several transcription factors and candidate regulatory genes involved in H2O2 transcriptional gene networks were identified. Comparisons with other publicly available transcriptome data sets of abiotically stressed Arabidopsis revealed an important intersection with H2O2-deregulated genes, positioning elevated H2O2 levels as an important signal within abiotic stress-induced gene expression. Finally, analysis of transcriptional changes in a combination of a genetic (catalase deficiency) and an environmental (high light) perturbation identified a transcriptional cluster that was strongly and rapidly induced by high light in control plants, but impaired in catalase-deficient plants. This cluster comprises the complete known anthocyanin regulatory and biosynthetic pathway, together with genes of hitherto unknown function.

# _embedded.samples[].characteristics.submission title[].text
Transcription profiling of control and catalase-deficient Arabidopsis (Arabidopsis thaliana) plants

# _embedded.samples[].organization[].Name
GSF-NRCEH Biochem. Plant Path. Neuherberg - German

# _embedded.samples[].organization[].Name
VIB Department of Plant Systems Biology, Ghent University, Belgium

# _embedded.samples[].organization[].Name
VIB Department of Plant Systems Biology, Ghent University, Belgium

# _embedded.samples[].organization[].Name
VIB Department of Plant Systems Biology, Ghent University, Belgium

# _embedded.samples[].characteristics.submission description[].text
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

# _embedded.samples[].characteristics.submission title[].text
Genes and miRNAs regulated by Gadd45a during somatic cell reprogramming

# _embedded.samples[].organization[].Name
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science

# _embedded.samples[].organization[].Name
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science

# _embedded.samples[].characteristics.submission description[].text
The long-standing view of 'immortal germ line versus mortal soma' poses a fundamental question in biology concerning how oocytes age in molecular terms. A mainstream hypothesis is that maternal aging of oocytes has its roots in gene transcription. Investigating the proteins resulting from mRNA translation would reveal how far the levels of functionally available proteins correlate with mRNAs, and would offer novel insight into the changes oocytes undergo during maternal aging. Gene ontology semantic analysis reveals the high similarity of the detected proteome (2,324 proteins) to the transcriptome (22,334 mRNAs), though not all proteins have a cognate mRNA. Concerning their dynamics, 4-fold changes of abundance are more frequent in the proteome (3%) than the transcriptome (0.05%), with correlation. Whereas proteins associated with the nucleus (e.g. structural maintenance of chromosomes, spindle-assembly checkpoints) are largely represented among those that change in oocytes during maternal aging; proteins associated with oxidative stress/damage (e.g. superoxide dismutase) are infrequent. These quantitative alterations are either impoverishing or enriching. Using gene ontology analysis, these alterations do not relate in any simple way to the classic signature of aging known from somatic tissues. We conclude that proteome analysis of mouse oocytes may not be surrogated with transcriptome analysis, given the lack of correlation. Furthermore, we conclude that the classic features of aging may not be transposed from somatic tissues to oocytes in a one-to-one fashion. Overall, there is more to the maternal aging of oocytes than mere cellular deterioration exemplified by the notorious increase of meiotic aneuploidy. Three pools of 20 zona-enclosed B6C3F1 oocytes from each age group were subjected for experiment.

# _embedded.samples[].characteristics.submission title[].text
Maternal age effect on mouse oocytes: new biological insight from proteomic analysis

# _embedded.samples[].characteristics.submission description[].text
Here, we transferred GmDof4 from soybean (Glycine max), a transcription factor affecting content of lipid in Arabidopsis, into C. ellipsoidea and found that the expression of GmDof4 significantly enhanced the lipid content by maximum 57.21%, shifted the content of different fatty acids, but did not affect the growth of the host cells. Using the Solexa/Illumina-based RNA-Seq analysis, we found expression of GmDof4 significantly regulates 1,076 genes, of which 754 genes were up-regulated and 322 genes were down-regulated, under mixotrophic culture. This study provides a new way to improve the lipid of microalgae. The GmDof4 transgenic strain Dof4-1 and control (pCK transgenic line CK-1) were cultured in liquid antibiotic-free Endo medium at 25??? under illumination (100 ??mol photons m-2 s-1) for 120 h. Cells at a concentration of approximately 1?? 10^7 cells/mL were collected for library construction and sequencing using Illumina GAIIx.

# _embedded.samples[].characteristics.submission title[].text
Overexpression of GmDof4 from Soybean Significantly Enhances the Lipid Content of Chlorella ellipsoidea

# _embedded.samples[].characteristics.submission description[].text
Comparison of WT and efd-1 nodule transcriptome, using isolated nodules, at 4 and 10 dpi. Search of EFD possible targets by comparison of transcriptomes from empty vector-tranformed vs. 35S:EFD roots.

# _embedded.samples[].characteristics.submission title[].text
Transcription profiling of wild type, Mtefd-1 mutant and pPEX-35SMtEFD transformed Medicago truncatula root nodules at 4 and 10 days post innoculation with Sinorhizobium meliloti

# _embedded.samples[].characteristics.submission description[].text
Recent evidence suggests that ovarian high-grade serous carcinoma (HGSC) originates from the epithelium of the fallopian tube. However, most mouse models are based on the previous prevailing view that ovarian cancer develops from the transformation of the ovarian surface epithelium. Here, we report the extensive histological and molecular characterization of the mogp-TAg transgenic mouse, which expresses the SV40 large T-antigen (TAg) under the control of the mouse m??llerian-specific Ovgp-1 promoter. Histologic analysis of the fallopian tubes of mogp-TAg mice identified a variety of neoplastic lesions analogous to those described as precursors to ovarian HGSC. We identified areas of normal appearing p53-positive epithelium that are similar to ???p53 signatures??? in the human fallopian tube. More advanced proliferative lesions with nuclear atypia and epithelial stratification were also identified that were morphologically and immunohistochemically reminiscent of human serous tubal intraepithelial carcinoma (STIC), a potential precursor of ovarian HGSC. Beside these noninvasive precursor lesions, we also identified invasive adenocarcinoma in the ovary of 56% of the mice. Microarray analysis revealed several genes differentially expressed between the fallopian tube of mogp-TAg and WT C57BL/6. One of these genes, Top2a, which encodes topoisomerase II-alpha, was shown by immunohistochemistry to be concurrently expressed with elevated p53 and specifically elevated in mouse STICs, but not in surrounding tissues. TOP2A protein was also found elevated in human STICs, low-grade, and high-grade serous carcinoma. The mouse model reported here displays a progression from normal tubal epithelium to invasive HGSC in the ovary, and therefore closely simulates the current emerging model of human ovarian HGSC pathogenesis. This mouse therefore has the potential to be a very useful new model for elucidating the mechanisms of serous ovarian tumorigenesis, as well as for developing novel approaches for the prevention, diagnosis, and therapy of this disease. Keywords: transgenic mouse model, ovarian cancer, fallopian tube, intraepithelial carcinoma 6 mouse fallopian tubes (FT) were analyzed with experimental repeats; 3 wildtype C57BL6 mice (FT) and 3 transgenic mogp-TAg (FT), with one set of each at 7, 8 and 9 weeks of age.

# _embedded.samples[].characteristics.submission title[].text
A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high-grade serous carcinoma development

# _embedded.samples[].characteristics.submission description[].text
We generated a genome-wide map of 5hmC in rice panicle using a sensitive chemical labeling method to capture DNA fragments with 5hmC modification, followed by NGS sequencing. We showed that the 5hmC peaks distribution is non-random, about 52% 5hmC was located in gene bodies, 25% in intergenic regions, 11% in promoters, and 12% in immediate downstream. It was significantly enriched in heterochromatic regions of chromosomes 4 and 10, and especially located around TE genes. Combined with RNA-seq transcriptome data, we found that the gene-specific alterations of 5hmC can result in gene activation or repression, suggesting a potential role for 5hmC in gene regulation. From the compared distribution analysis among super-hybrid rice cultivars LYP9, and its parental lines 93-11 and PA64s, we investigated the cultivar-specificity of both the global levels and locus-specific distribution of 5hmC. Our data provided an overview of the genomic distribution of 5hmC in rice panicle. This will set the stage for further functional characterization of this novel DNA modification and its biosynthesis in rice. Examination of 5hmC modifications in rice panicle This submission represents ChIP-Seq component of study.

# _embedded.samples[].characteristics.submission title[].text
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine in rice

# _embedded.samples[].organization[].Name
Beijing Institute of Genomics, Chinese Academy of Sciences

# _embedded.samples[].organization[].Name
Beijing Institute of Genomics, Chinese Academy of Sciences

# _embedded.samples[].characteristics.submission description[].text
To identify QKI targets, we performed QKI knockdown in BEAS2B cells and analyzed alternative splicing patterns by high-throughput RNA sequencing. The mRNA profiles of control- and QKI-knockdown BEAS2B cells were generated by deep sequencing using Illumina GAIIx sequencer.

# _embedded.samples[].characteristics.submission title[].text
Genomewide analysis of QKI-dependent alternative splicing

# _embedded.samples[].organization[].Name
Shanghai Institutes for Biological Sciences

# _embedded.samples[].organization[].Name
Shanghai Institutes for Biological Sciences

# _embedded.samples[].characteristics.submission description[].text
We use a metabolic labeling strategy for directly measuring nucleosome turnover to determine the role of chromatin remodeler Chd1 on chromatin dynamics in mouse embryonic fibroblasts expressing with wildtype-Chd1 and dominant negative K510R-Chd1. We find that expression of K5 10R-Chd1 decreases nucleosome turnover at the promoter and increases turnover within the gene body. 10 Illumina sequencing samples and 4 Nimblegen array samples

# _embedded.samples[].characteristics.submission title[].text
The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 [HiSeq]

# _embedded.samples[].characteristics.submission description[].text
Transcriptional profiling of p16-induced senescent human diploid fibroblasts compared with proliferating cells. TIG-3 ER-p16 cells (primary normal human diploid fibroblasts expressing a 4-hydroxytamoxifen(4-OHT) regulatable form of human p16) were cultured for 7 days with or without 4-OHT. Total RNA was isolated using TRIzol reagent and were analyzed using the hum

# _embedded.samples[].characteristics.submission title[].text
Gene expression profile of p16-induced senescence in normal human diploid fibroblasts.

# _embedded.samples[].characteristics.submission description[].text
The transcriptional repressor Zbtb20 is essential for specification of hippocampal CA1 pyramidal neurons. Moreover, ectopic expression of Zbtb20 is sufficient to transform subicular and retrosplenial areas of D6/Zbtb20S mice to CA1. We used microarrays to identify genes that are repressed by Zbtb20 in developing CA1 pyramidal neurons in the CA1-transformed cortex of D6/Zbtb20S mice. For RNA extraction and hybridization on Affymetrix microarrays, we isolated the CA1-transformed subiculum and retrosplenial cortex from postnatal day 1 D6/Zbtb20S mice, as well as corresponding areas from their wildtype littermates. Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen). Each RNA sample represents a pool of RNA obtained from dissected tissues of seven animals.

# _embedded.samples[].characteristics.submission title[].text
Zbtb20-mediated repression of genes in developing CA1 pyramidal neurons

# _embedded.samples[].characteristics.submission description[].text
This study investigated the alternative gene, protein expression and morphological changes of L. monocytogenes 08-5923 following 15min, 4h and 30h exposure to bacteriocin carnocyclin A (cclA). The microarray experiment studied the gene expression of untreated and treated Listeria cells following 4h exposure to cclA. A six chip study using total RNA recovered from six separate cultures of L. monocytogenes 08-5923; three grown in TSB (untreated) and three grown in TSB with cclA (treated); Each chip measures the expression level of 2,857 genes from L. monocytogenes 08-5923 with five 60-mer probe pairs (PM/MM) per gene, with 1-fold technical redundancy.

# _embedded.samples[].characteristics.submission title[].text
Stress and adaptation of Listeria monocytogenes 08-5923 exposed to a sublethal dose of carnocyclin A

# _embedded.samples[].characteristics.submission description[].text
1, Using mRNA-Seq to get expression profiling of rrp6l1-2 mutant and Col-0 wild-type (WT); 2,Using MethylC-Seq to provide single-base resolution of DNA methylation status in rrp6l1-2 mutant; 3, Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of rrp6l1-2 and WT mRNA-Seq: 2 samples examined, WT and rrp6l1-2 mutant; MethylC-Seq: 1 sample examined, rrp6l1-2 mutant; small RNA-Seq: 2 samples examined, WT and rrp6l1-2 mutant

# _embedded.samples[].characteristics.submission description[].text
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

# _embedded.samples[].characteristics.submission title[].text
MOV10 Is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3'UTRs

# _embedded.samples[].characteristics.submission description[].text
High resolution ChIP-seq mapping, supported by in vitro reconstitution studies, suggests that the Cse4 nucleosome is a hemisome that occupies the ~80-bp AT-rich CDEII sequence. H4S47C-anchored cleavage mapping of S. cerevisiae centromeres

# _embedded.samples[].characteristics.submission title[].text
The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo

# _embedded.samples[].characteristics.description[].text
From June to August 2011, soil cores were repeatedly collected at 5 pine forest sites in northern Bavaria, Germany (Table S1). In total, 19 soil cores were collected by using a boring rode (6 cm diam.), from plots with or without Ericacean plants in the understory. The organic layers Oe (partly humified organic layer) and Oa (black, amorphous organic layer) as well as the mineral soil horizons Ah (bleached, dark grey mineral horizon) and E (bleached, pale grey mineral horizon) were separated. The Oe layer was further subdivided into an upper and lower Oe if its thickness exceeded 5 cm. Macroinvertebrates, roots and larger fragments like parts of pine cones were removed and 30 ml of each layer was transferred to two 15 ml tubes for transport. In the laboratory, half of each sample was weighed and dried (60 °C) to constant dry mass in a drying closet for determination of the dry weight. The dried material was subsequently homogenized and used to measure carbon (C) and nitrogen (N) contents in a Multi N/C 2100 analyzer (Analytik Jena, Germany). Based on these data and the thickness of each layer, the changes in C/N ratios per cm depth of the Oe (ΔC/N cm-1) were calculated. Subsamples of 5 g were extracted in 1.0 M KCl solution (soil/solution ratio 1:10), shaken on a horizontal shaker at 225 min-1 for 1h and subsequently filtered (cellulose folded filters 5951/2, 4-7 µm, Whatman, Germany). NH4+ and of NO3- concentrations in the filtered KCL extracts were determined using colorimetric flow injection analysis (FIA-LAB, MLE, Dresden). Activities of enzymes involved in the degradation of the major plant components cellulose (β-glucosidase) and lignin (phenoloxidases) as well as degradation of chitin (chitinase) were comparatively analysed using a 96-well microplate-based system. The activity of the hydrolytic enzymes beta-glucosidase and chitinase were measured using fluorescence photometry subsequent to incubation with 4-methylumbelliferone (MUF) esters (Pritsch et al. 2004). The activity of phenoloxidases was measured using spectrophotometry after incubation with the artificial substrate ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid)). To avoid artificial conditions affecting the enzyme activities, the substrate was directly added to the untreated soil without homogenization or addition of buffer solutions. Concentration of total phenolic hydroxyl groups was measured by applying the Folin-Ciocalteu method (Folin & Ciocalteu, 1927), modified according to Bärlocher & Graça (2005). Extracted phenolic compounds were treated with Folin-Ciocalteau reagent and measured with a spectrophotometer (NanoDrop ND-1000 spectrophotometer, Thermo Fisher Scientific Inc., Los Angeles, U.S.A.) at 750 nm. Phenolic content was calculated based on a calibration series with tannic acid (Riedel-de Haën, Seelze, Germany) and expressed as g tannic acid equivalents (TAE) per mg of soil dry mass. Four subsamples of 0.3 g each were weighed from the Oe layer for DNA extraction. DNA was extracted from the soil samples according to Peršoh et al. (2008). Therefor, 300 μl of Al2(SO4)3 (0.4 M) were applied to flocculate humic compounds prior to cell disruption. The fungal ITS1 region was amplified using the Primers ITS1F (5’-CTTGGTCATTTAGAGGAAGTAA, Gardes and Bruns 1993) and ITS1Univ-R (5’-GCTGCGTTCTTCATCGATGC, White et al. 1990). Primers of each pair were extended by one of 19 different sample identifier sequences (SIDs) of 10 bp in length at the 5’-ends. Each polymerase chain reaction (PCR) batch of 25 μl in total included 15.65 μl H2O, 0.75 μl MgCl2 (50 mM), 2.5 μl 10× PCR buffer (Invitrogen), 2.5 μl dNTPs (2 mM), 1.25 μl of each primer (10 μM), 0.1 μl Taq polymerase (5 U/μl, Invitrogen), and 1 μl DNA extract. Cycling reactions started with an initial denaturation of 2 min at 95°C followed by 35 cycles of 20 s at 94°C (denaturation), 1 min at 61°C (annealing), 2 min at 72°C (elongation) and finished with an extension step of 15 min at 72°C. PCR products were purified using the ExoSAP-IT® kit (Affymetrix) and the relative DNA concentration was assed evaluating images of Agarose gels (0.8%) after electrophoresis (2 µl PCR product and 1 µl of λ-Pst1 DNA ladder) using GeneTools (Syngene). PCR-products were equimolarly pooled and sent on dry ice to GATC (Konstanz, Germany) for 454-pyrosequencing analyses. The 11 525 obtained sequences were assembled to contigs using CLC Genomics Workbench (CLC bio), applying a bubble size of 50 and a minimum contig length of 110. Contigs of at least 90% similarity were initially grouped using the R package ‘RFLP Tools’ R (v2.11.1, www.r-project.org) and revised in BioEdit (v7.1.9, www.mbio.ncsu.edu/BioEdit) by creating consensus sequences of similar sequences (≥ 99% similarity). Groups of which either the 5’-end of the 18S rRNA or the 3’-end of the 5.8S rRNA could not be located were analyzed in detail by downloading and aligning similar sequences. These ambiguous sequences were only retained if they definitely represented non-chimeric ITS1 sequences. Altogether, ITS1 regions were identified and extracted from 187 contigs. These served as reference sequences, against which all 11 525 original sequences were mapped with thresholds for coverage and similarity set to 30% and 95%, respectively. Reference sequences were assigned to operational taxonomic units (OTUs) by grouping full length ITS1 sequences of at least 97% similarity. The abundance of each OTU in each sample was indicated by the number of original sequences successfully mapped to the reference sequences, which applied for 10 812 sequences in total. Names were assigned to OTUs by evaluating BLAST results as detailed previously (Peršoh et al. 2010). Briefly, the GenBank database (www.ncbi.nlm.nih.gov) was searched by BLAST and all hits which attained at least 90% of the best alignment score were considered for name assignment. A taxonomic level unifying all names under which the related sequences were deposited was chosen as name for each OTU. Environmental sequences and clearly outlying names were disregarded, but documented as ambiguities and outliers, respectively. Based on their taxonomic affiliation, OTUs were categorized as ectomycorrhizal (ECM), and ericoid mycorrhizal fungi (ERM). Comparisons with the sequences of Archeorhizomycetes (ARM, Rosling et al. 2011) were conducted separately to identify representatives of this group. To assess the putative biology of the 4 OTUs accounting for more than 3% of all sequences, but neither assignable to ARM, nor representing ECM or ERM fungi, the origin of all best sequences was established. Thereby, OTUs with >95% of the relatives not originating from living organisms were categorized as saprotrophic. This applied to 3 of the 4 OTUs. A matrix coding the abundance of each OTU in each subsample was imported in Primer6 (Plymouth Routines) and abundances within samples were standardized by total. Bray Curtis similarity was applied to calculate similarities among samples. Analyses of Similarity (ANOSIM) were used to elucidate if the understory vegetation had an impact on composition of fungal community as a whole, on the ARM community, and on the ECM, ERM, and saprobic communities. Similarities among samples were visualized by non-metric multidimensional scaling. Correlations among distribution patterns of OTUs, C/N ratios and contents, N fractions, and enzyme activities were assessed by calculating Pearson Product Moment Correlations of Log10 + 1 transformed data using the software R version 2.13.1. References Bärlocher, F, Graça, MAS (2005). Total phenolics. In: Graça, MAS , Bärlocher, F , Gessner, MO (eds.). Methods to study litter decomposition - A practical guide. Springer pp 97-100. Folin, O, Ciocalteu, V (1927). On tyrosine and tryptophane determination in proteins. J Biol Chem 27, 239-343. Gardes M, Bruns TD (1993). ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113-118. Peršoh D, Theuerl S, Buscot F, Rambold G (2008). Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil. J Microbiol Methods 75: 19-24. Peršoh D, Melcher M, Flessa F, Rambold G (2010). First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum and its host Pinus sylvestris. Fungal Biol 114: 585-596. Pritsch K, Raidl S, Marksteiner E, Blaschke H, Agerer R, Schloter M, Hartmann A (2004). A rapid and highly sensitive method for measuring enzyme activities in single mycorrhizal tips using 4-methylumbelliferone-labelled fluorogenic substrates in a microplate system. J Microbiol Methods 58, 233-241. Rosling A, Cox F, Cruz-Martinez K, Ihrmark K, Grelet G-A, Lindahl BD et al (2011). Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi. Science 333: 876-879. White TJ, Bruns T, Lee S, Taylor J (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Shinsky JJ, White TJ (eds). PCR Protocols: A Guide to Methods and Applications. Academic Press. pp 315-322.

# _embedded.samples[].characteristics.submission description[].text
19 uncultured fungus samples from ENA SRA

# _embedded.samples[].characteristics.submission title[].text
19 uncultured fungus samples from ENA SRA

# _embedded.samples[].characteristics.submission description[].text
Analysis of gene expression in lung and prostate cancer cells expressing non-target (NT), p44/wdr77. or PRMT5 shRNA. Results provide important information on how p44/wdr77 and PRMT5 control cellular proliferation. Total RNA obtained from cells expressing NT, p44/wdr77, or PRMT5 shRNA.

# _embedded.samples[].characteristics.submission title[].text
Genome-wide analysis of genes regulated by p44/wdr77 and PRMT5 in lung and prostate cancer cells

# _embedded.samples[].characteristics.submission description[].text
We performed genome wide transcriptome analyses of a large cohort human kidney tubule samples.

# _embedded.samples[].characteristics.submission description[].text
To investigate targets of miR-582-5p that which might participate in the transition to CRPC, we evaluated the gene expression profiles of LNCaP miR-582-5p cells and LNCaP EV cells using DNA microarray analysis. We evaluated the gene expression profiles of LNCaP miR-582-5p cells and LNCaP EV cells using DNA microarray with GeneChip?? Human Gene 1.0 ST array.

# _embedded.samples[].characteristics.submission title[].text
Gene expression profiles of LNCaP miR-582-5p cells and LNCaP empty vector cells.

# _embedded.samples[].characteristics.submission description[].text
The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilization wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the 7th cleavage and extending beyond the MBT at the 12th cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal genes whose mRNAs are deadenylated shortly after fertilization, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organization of gene regulatory networks in the early Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization

# _embedded.samples[].characteristics.submission title[].text
High-resolution analysis of gene activity during the Xenopus mid-blastula transition

# _embedded.samples[].organization[].Name
MRC National Institute for Medical Research

# _embedded.samples[].organization[].Name
MRC National Institute for Medical Research