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Genomics
Palm genera nuclear phylogenomics
PRJNA1131474 | ENA
GenomicsA somatic reference standard for cancer genome sequencing with COLO829
Identification of somatic alterations in cancer has become feasible with the massive adoption of next generation sequencing. However, due to variability in sequencing and informatics pipelines, a common somatic reference is needed. We thus performed paired whole genome sequencing of a metastatic mel...
EGAS00001001385 | EGA
TranscriptomicsRNAseq in quiescent and refed quiescent cells in Saccharomyces cerevisiae
Gradient-enriched quiescent cells of a 6 days stationary phase culture were refed with rich medium (Yeast Peptone Dextrose 2%) in the presence or absence of RNAPII inhibition by various means (rpb1-1 thermosensitive mutant, thiolutin). Samples were harvested in quiescence and 30 minutes post-refeedi...
ORGANISM(S): Saccharomyces cerevisiae 
2025-07-26 | E-MTAB-14983 | biostudies-arrayexpress
ProteomicsHIV-1 Nef Reprograms Neuronal Lipid Rafts to Drive Neuroinflammation and Neurodegeneration in HIV-associated Neurocognitive Impairment
HIV-associated neurological disorders (HAND) remain a common co-morbidity of HIV infection. HIV protein Nef has been shown to increase the abundance of neuronal lipid rafts - cholesterol- and sphingolipid-rich membrane microdomains implicated in neurodegeneration and neuroinflammation. Here, we inve...
ORGANISM(S): Homo sapiens (Human) 
2026-03-23 | PXD065713 | Pride
Nef Exosomes. Neurons Hiv Hiv-associated neurological disorder Lipid rafts Neurodegeneration 
Genomicsena-DATASET-TGEN-24-05-2016-20:32:03:406-20 - samples
Paired PCR-free whole genome sequencing data of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. The data was generated with mean mapped coverages of 99X for COLO829 a...
EGAD00001002142 | EGA
GenomicsDATA-291 - samples
This paper describes the work by Akbari V,. et al. on detection of allele specific methylation using oxford nanopore sequencing data. They have developed set of tools, SNVoter and NanoMethPhase, and workflow which enable the detection of allele specific methylation even in samples with sparse covera...
EGAD00001007920 | EGA
TranscriptomicsAged Mice are Unable to Mount an Effective Myeloid Response to Sepsis
Old C57BL/6 mice cannot mount an effective innate immune response We used mouse microarrays to detail the molecular profile of the events that occur following infection
ORGANISM(S): Mus musculus 
2014-02-04 | E-GEOD-51925 | biostudies-arrayexpress
GenomicsThe Ovarian Cancer Association Consortium Data Access Committee
Data Access Committee EGAC00001000616
EGAC00001000616 | EGA
TranscriptomicsscRNAseq in quiescent and refed quiescent cells in Saccharomyces cerevisiae
The main objective of this project is the characterization of cell-to-cell transcriptional heterogeneity in and out of the yeast quiescent state. Do quiescent cells manage to respond rapidly to their environment through a general transcriptional permissiveness, or through a cell- to-cell heterogenei...
ORGANISM(S): Saccharomyces cerevisiae 
2025-07-26 | E-MTAB-14980 | biostudies-arrayexpress
GenomicsData Access Committee for COLO829 Somatic reference standard for cancer genome sequencing
Data Access Committee EGAC00001000408
EGAC00001000408 | EGA
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