Ontology highlight
ABSTRACT:
PROVIDER: PRJNA832021 | ENA |
REPOSITORIES: ENA
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Project description:Arabidopsis sequencing mature polle DNA-Seq data
| PRJNA791194 | ENA
Project description:Seeds are comprised of three major parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. Each seed part undergoes distinct developmental programs during seed development. What methylation changes occur in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of two major parts of Arabidopsis mature green stage seeds, the seed coat and embryo, using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from two parts of Arabidopsis mature green seeds: seed coat (SC) and embryo (EMB).
2014-05-17 | E-GEOD-57755 | biostudies-arrayexpress
Project description:Genomewide DNA methylation profiles, generated by MeDIP-seq, for 8.5dpc wildtype and Dnmt3l-/+ mouse embryos were compared to identify differentially methylated regions (DMRs) that depend on the activity of the de novo DNA methyltransferase cofactor Dnmt3l in the oocyte. These DMRs were further characterised by their methylation state in mature mouse sperm and in the livers of inter-subspecies newborn mice. Maternal ICRs were identified by hypomethylation in Dnmt3l-/+ embryos as well as sperm, and maternal allele-specific methylation in liver. MeDIP-seq for two pools of wildtype and two pools of Dnmt3l-/+ mouse 8.5dpc embryos, the sperm of three sires, and 12 pools of three different embryonic livers each. Sliding window read count comparison between wildtype and Dnmt3l-/+ embryos, and between wildtype embryos and sperm samples. Read count comparison between the parental alleles at known SNP sites in inter-subspecies liver data.
2012-10-04 | E-GEOD-32687 | biostudies-arrayexpress
Project description:In order to discover novel small RNAs expressed in mature sperm, we isolated mature sperm from mouse cauda epididymis, comparing with data from adult tesis and uterus. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA of mature sperm, testis and uterus of mice. RNAs extracted from mature sperm, adult testis and uterus were used for high throughput sequencing analysis
2013-01-31 | E-GEOD-38702 | biostudies-arrayexpress
Project description:Mammalian embryonic stem (ES) cells and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ES cells and sperm. In ES cells, we recover well-characterized features of chromatin such as promoter nucleosome depletion, and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies. We document global differences in nuclease accessibility between ES cells and sperm, finding that the majority of histone retention in sperm preferentially occurs in large gene-poor genomic regions, with only a small subset of nucleosomes being retained over promoters of developmental regulators. Finally, we describe evidence that CTCF remains associated with the genome in mature sperm, where it could play a role in organizing the sperm genome. We use Micrococcal Nuclease (MNase) to map chromatin structure in mouse ES cells and sperm. Specifically, we generate paired-end deep-sequencing libraries that are able to distinguish DNA digestion products by size, thus allowing us to simultaneously map nucleosomes as well as other DNA-binding proteins such as transcription factors.
2014-07-08 | E-GEOD-58101 | biostudies-arrayexpress
Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
2020-06-01 | MODEL2003240001 | BioModels
Project description:To determine how the genome is packaged in C. elegans sperm, we isolated adult him-8(e1489) males and collected mature sperm (~99% purity). We utilized micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq) to evaluate the presence of nucleosomes across the genome in sperm vs. early embryos. We found that the sperm genome retains nucleosomes genome-wide, comparable to wild-type early embryos.
2018-07-23 | GSE115705 | GEO
Project description:As nucleosomes are widely replaced by protamine in mature human sperm, epigenetic contributions to embryo development appear limited. However, our genome-wide approaches find nucleosomes at low levels genome-wide, but also significantly enriched at imprinted gene clusters, miRNA clusters, HOX gene clusters, and the promoters of other developmental transcription and signaling factors. Developmental promoters were often DNA hypomethylated, and bore histone modifications localized to discrete locations: H3K4me2 is enriched at certain developmental promoters, whereas large blocks of H3K4me3 localize to a subset of developmental promoters, regions in HOX loci, certain non-coding RNAs, and generally to paternally-expressed imprinted loci. In contrast, H3K4me3 is generally absent at paternally-repressed imprinted loci. Interestingly, repressive H3K27me3 is enriched at many developmental promoters that lack early expression in embryos, with significant overlap with bivalent (H3K4me3/H3K27me3) promoters in ES cells. Taken together, epigenetic marking in sperm is extensive, and correlated with developmental regulators. *Use of ChIP-seq to identify regions enriched for histone, and several histone variants in human sperm. *Histone Localization: Chromatin was prepared from 40 million sperm as described previously (1) in the absence of crosslinking reagent, treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were gel purified (~140-155 bp) for sequencing and array analysis. Mononucleosomes for ChIP-seq were sequenced from a single donor (3 replicas combined) or a donor pool (4 donors each ~6 million reads) and data was normalized to 20 million input control reads (pooled donor sperm genomic DNA). *Chromatin IP and Preparation for Genomics Methods: ChIP methods were as described previously (2) but were performed without a cross linking agent and slight modifications to the salt levels, 250 mM NaCl, 200 mM LiCl, and replaced the TE wash with 150 mM PBS wash. A subset of the modifications H3K4me3, H3K27me3 and H2A.z were done from a donor pool and only analyzed by Solexa. Each IP was repeated three time and the three replicas were pooled. For sequencing, DNA lengths corresponding to mononucleosomes with adapters (220-280 bp) were gel purified after the addition of the Illumina adaptors. The sequencing data was normalized to histone donor pool (D1 was subsampled to 5million and combined with the reads from D2-D4). 1. Zalenskaya, I.A., Bradbury, E.M. & Zalensky, A.O. Chromatin structure of telomere domain in human sperm. Biochem Biophys Res Commun 279, 213-8 (2000). 2. Gordon, M. et al. Genome-Wide Dynamics of SAPHIRE, an Essential Complex for Gene Activation and Chromatin Boundaries. Mol Cell Biol 27, 4058-69 (2007). Samples corresponding to each GSE15690_Seq* processed data supplementary file: GSE15690_Seq_H2AZ.txt: GSM392695 GSE15690_Seq_H3K27Me3.txt: GSM392699, GSM392700 GSE15690_Seq_H3K4Me3.txt: GGSM392696-GSM392698 GSE15690_Seq_HistoneMnase_D1.txt: GSM392701-GSM392707, GSM392714-GSM392716 GSE15690_Seq_HistoneMnase_PooledDonor.txt: GSM392708-GSM392713, GSM392717-GSM392720
2009-06-15 | E-GEOD-15690 | biostudies-arrayexpress
Project description:In order to discover novel small RNAs expressed in mature sperm, we isolated mature sperm from mouse cauda epididymis, comparing with data from adult tesis and uterus. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA of mature sperm, testis and uterus of mice.
2013-01-31 | GSE38702 | GEO
Project description:During sexual reproduction in flowering plants, the two haploid sperm cells embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome level. While the transcriptome of pollen and sperm cells in Arabidopsis thaliana is well documented, previous analyses were mostly based on expression at gene level. In-depth transcriptome analysis, particularly the extent of alternative splicing at the resolution of sperm cell and vegetative nucleus was still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis sperm cells and vegetative nuclei isolated from mature pollen grains. Based on our de-novo transcriptome assembly we identified 58039 transcripts, including 9681 novel transcripts, of which 2091were expressed in sperm cells and 3600 in vegetative nuclei. Our data from sperm cell and vegetative nucleus identified 468 genes that were regulated both at gene and splicing level, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides novel insights into a gamete specific alternative splicing landscape at unprecedented resolution.
2022-12-14 | GSE201115 | GEO