Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA388880 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5641810.fastq.gz | Fastqsanger.gz | |||
| SRR5641811.fastq.gz | Fastqsanger.gz | |||
| SRR5641812.fastq.gz | Fastqsanger.gz | |||
| SRR5641813.fastq.gz | Fastqsanger.gz | |||
| SRR5641804.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:The composition and dynamics of tightly bound chromatin associated RNAs during mitosis remains elusive. Here we report identification of chromatin enriched (cheRNAs) by biochemical nuclear fractionation coupled with RNA-seq in both interphase and mitotic phase of A549 and HeLaS3 cell lines. We show that highly abundant cheRNAs, mostly small noncoding RNAs, are largely maintained in mitotic chromatin, and constitute a substantial part of chromatin throughout cell cycle. We also show that the mitotic retained cheRNAs tend to be cell type nonspecific. We speculate that these cell type nonspecific cheRNAs might play roles in chromatin state and gene expression control. We anticipate the panoramic landscape of RNA composition of chromatin both in interphase and M-phase would shed light on understanding the structure and function of chromatin in M phase and would also help the understanding of some fundamental biological functions.
2022-10-05 | GSE99594 | GEO
Project description:Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA.
2015-03-04 | GSE66478 | GEO
Project description:Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA. Nuclei from three biological replicates were isolated by detergent lysis, fractionated, then three chromatin and three soluble RNA samples were converted to cDNA using Illumina TruSeq stranded protocol, and sequenced on Illumina HiSeq2000
2015-03-04 | E-GEOD-66478 | biostudies-arrayexpress
Project description:Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA
| PRJNA277042 | ENA
Project description:Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that they could provide transcriptional memory through mitosis. To obtain the first genome-wide view of the dynamics of chromatin structure during mitosis, we compared the DNase sensitivity of interphase and mitotic chromatin at two stages of cellular maturation in a rapidly dividingmurine erythroblastmodel. Despite global chromosome condensation visible during mitosis at the microscopic level, the chromatin accessibility landscape is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility, whereas distal regulatory elements preferentially lose accessibility. Promoters with the highest degree of accessibility preservation in mitosis tend to also be accessible across many murine tissues in interphase. Transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but does not visibly influence mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis and are modulated at the level of individual genes and regulatory elements. Dnase-Seq data is integrated with Chip-seq [GSE36589, GSE30142] and RNA-seq to examine epigentic changes in mitosis. We performed DNase-seq on two cell lines, G1E and G1E-ER4, both on an asynchronus population, and on a sample of cells in mitosis; each of the 4 experiments in triplicate.
2014-10-01 | E-GEOD-61885 | biostudies-arrayexpress
Project description:Biochemical fractionation of HL-1 mouse cardiomyocyte nuclei and RNA-seq of chromatin-enriched and soluble-nuclear RNA
2023-12-31 | GSE164126 | GEO
Project description:We have used a combination of chemical genetics, chromatin proteomics and imaging to map the earliest chromatin transactions during vertebrate cell entry into mitosis. Chicken DT40 Cdk1as cells undergo synchronous mitotic entry within 15 minutes following release from a 1NM-PP1-induced arrest in late G2. In addition to changes in chromatin association with nuclear pores and the nuclear envelope, earliest prophase is dominated by changes in the association of ribonucleoproteins with chromatin, particularly in the nucleolus, where pre-rRNA processing factors leave chromatin significantly before RNA polymerase I. Nuclear envelope barrier function is lost early in prophase and cytoplasmic proteins begin to accumulate on the chromatin. As a result, outer kinetochore assembly appears complete by nuclear envelope breakdown (NEBD). Most interphase chromatin proteins remain associated with chromatin until NEBD, after which their levels drop sharply.
2022-01-31 | PXD026385 | Pride
Project description:Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces acting on chromatin. Mitotic cell division induces drastic chromatin condensation, but following reentry into the G1 cell cycle phase, condensed chromosomes unwind to re-establish interphase organization. Here, we use a cell line allowing auxin-mediated degradation of RNA polymerase II to test its role in this transition. In situ Hi-C and super-resolution imaging showed that RNAPII is required for compartment and loop formation following mitosis. RNAPs also often counteract loop extrusion and, in their absence, longer and more prominent loops arise. Evidence from chromatin fractionation and in silico modeling attribute these effects to RNAPII-mediated cohesin loading at active promoters upon G1 reentry. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.
2021-06-18 | GSE176285 | GEO
Project description:Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces acting on chromatin. Mitotic cell division induces drastic chromatin condensation, but following reentry into the G1 cell cycle phase, condensed chromosomes unwind to re-establish interphase organization. Here, we use a cell line allowing auxin-mediated degradation of RNA polymerase II to test its role in this transition. In situ Hi-C and super-resolution imaging showed that RNAPII is required for compartment and loop formation following mitosis. RNAPs also often counteract loop extrusion and, in their absence, longer and more prominent loops arise. Evidence from chromatin fractionation and in silico modeling attribute these effects to RNAPII-mediated cohesin loading at active promoters upon G1 reentry. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.
2021-06-18 | GSE176284 | GEO
Project description:Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces acting on chromatin. Mitotic cell division induces drastic chromatin condensation, but following reentry into the G1 cell cycle phase, condensed chromosomes unwind to re-establish interphase organization. Here, we use a cell line allowing auxin-mediated degradation of RNA polymerase II to test its role in this transition. In situ Hi-C and super-resolution imaging showed that RNAPII is required for compartment and loop formation following mitosis. RNAPs also often counteract loop extrusion and, in their absence, longer and more prominent loops arise. Evidence from chromatin fractionation and in silico modeling attribute these effects to RNAPII-mediated cohesin loading at active promoters upon G1 reentry. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.
2021-06-18 | GSE160317 | GEO