Ontology highlight
ABSTRACT:
PROVIDER: PRJNA769197 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR16229324_1.fastq.gz | Fastqsanger.gz | |||
| SRR16229325_1.fastq.gz | Fastqsanger.gz | |||
| SRR16229325_2.fastq.gz | Fastqsanger.gz | |||
| SRR18919841_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 5 |
Similar Datasets
Project description:Metroxylon sagu isolate:SAGO2022 Genome sequencing
| PRJNA660601 | ENA
Project description:Transcriptome analysis of Trunking and Non-trunking Metroxylon sagu leaf tissue
| PRJNA781491 | ENA
Project description:Spatial genome organization is essential to direct fundamental DNA-templated biological processes (e.g. transcription, replication, and repair), but the 3D in situ nanometer-scale structure of accessible cis-regulatory DNA elements within the crowded nuclear environment remains elusive. Here, we combined the recently developed Assay for Transposase-Accessible Chromatin with visualization (ATAC-see), PALM super-resolution imaging and lattice light-sheet microscope (a method termed 3D ATAC-PALM) to selectively image and quantitatively analyze key features of the 3D accessible genome in single cells. 3D ATAC-PALM reveals that accessible chromatin are non-homogeneously organized into spatially segregated clusters or accessible chromatin domains (ACDs). To directly link imaging and genomic data, we optimized multiplexed imaging of 3D ATAC-PALM with Oligopaint DNA-FISH, RNA-FISH and protein fluorescence. We found that ACDs colocalize with active chromatin and enclose transcribed genes. By applying these methods to analyze genetically purterbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight the 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.
2020-01-29 | GSE126112 | GEO
Project description:H3K4me3 profiling of OSCC secondary (2ary) recipient primary tumors (PTs) following in vivo exposure to control (CTRL) or palm oil-enriched (PALM) diet in primary recipient mice
2021-11-16 | GSE149047 | GEO
Project description:Epigenetic signatures of alm and assoication with outcome. Background: Acral melanoma (AM) is a rare, aggressive type of cutaneous melanoma (CM) with a distinct genetic profile for which comprehensive genome-wide methylation analysis (GWMA) is lacking. We aimed to identify a methylome signature distinguishing primary acral lentiginous melanoma (PALM) from primary non-lentiginous AM involving the acral sites (NALM), metastatic ALM (MALM), primary non-acral CM (PCM), and acral nevus (AN). Methods: A total of 22 PALM, 9 NALM, 10 MALM, 9 PCM, and 3 AN cases were subjected to GWMA using the Illumina Infinium Methylation EPIC array interrogating 866,562 CpG sites, and their methylomes were compared. Results: A prominent finding was that the methylation profiles of PALM and NALM were distinct, although both are considered canonical AMs. Four of the genes most differentially methylated between PALM and NALM or PALM and MALM were HHEX, DIPK2A (formerly C3orf58), NELFB (formerly COBRA1), and TEF. However, when primary AMs (PALM+NALM) were compared with MALM, IFITM1 and SIK3 were the most differentially methylated, highlighting their pivotal role in the metastatic potential of AMs. Patients with NALM had significantly worse disease-specific (DSS) and overall survival than patients with PALM. Aberrant methylation was significantly associated with aggressive clinicopathologic parameters, including greater Breslow thickness, ulceration, increased mitotic rate, and lymph node metastasis, and with worse DSS. Conclusion: Our study emphasizes the importance of distinguishing the two epigenetically distinct subtypes of AM. We also identified novel epigenetic prognostic biomarkers that may serve to risk-stratify patients with AM. These epigenetic alterations may be leveraged for development of targeted therapies.
2020-02-03 | GSE133395 | GEO
Project description:Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.
2021-10-23 | GSE186394 | GEO