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GenomicsDCC_R27_WGS_Runs.1 - samples
Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls
EGAD00001003909 | EGA
GenomicsDCC_R27_WGS_Runs.4 - samples
Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls
EGAD00001003975 | EGA
GenomicsDCC_R27_WGS_Runs.3 - samples
Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls
EGAD00001003957 | EGA
TranscriptomicsChimeraScan: A tool for identifying chimeric transcription in sequencing data
Next Generation Sequencing technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts. Thre...
ORGANISM(S): Homo sapiens 
2011-09-01 | E-GEOD-29098 | biostudies-arrayexpress
MetabolomicsSex-specific effects of CD248 on metabolism and the adipose tissue lipidome

Cd248 has recently been associated with adipose tissue physiology, demonstrated by reduced weight gain in high fat diet-fed mice with genetic deletion of Cd248 relative to controls. Here we set out to determine the metabolic consequences of loss of Cd248. Strikingly, we find these to be sex speci...

2023-01-05 | MTBLS6615 | MetaboLights
TranscriptomicsPronounced and Extensive Microtubule Defects in a Saccharomyces cerevisiae DIS3 Mutant
The recently proposed exozyme hypothesis posits that subunits of the RNA processing exosome assemble into structurally distinct protein complexes that function in disparate cellular compartments and RNA metabolic pathways. Here, in a genetic test of this hypothesis, we examine the role of Dis3 -- a...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-01 | E-GEOD-29018 | biostudies-arrayexpress
TranscriptomicsGene profiling of TRA1 and tra1-L3733A
Tra1 is a component of the Saccharomyces cerevisiae SAGA and NuA4 complexes and a member of the phosphatidylinositol 3-kinase kinase family that contain a C-terminal PI3K domain followed by a 35-residue FATC domain. We analyzed alleles with single residue changes in the FATC domain. Of these tra1-L3...
ORGANISM(S): Saccharomyces cerevisiae 
2010-09-19 | E-GEOD-18591 | biostudies-arrayexpress
TranscriptomicsGenomic expression over batch growth of mupirocin producing strain Pseudomonas synxantha NCIMB10586
The Pseudomonas synxantha strain NCIMB10586 produces the antibiotic mupirocin / Pseudomonic acid A from a 75 kb gene cluster; expression of this is regulated through quorum-sensing. We wished to examine expression of the strain during batch growth, in particular of the mupirocin cluster and any othe...
ORGANISM(S): Pseudomonas synxantha 
2021-06-04 | E-MTAB-10255 | biostudies-arrayexpress
GenomicsChromatin immunoprecipitation with next generation sequencing (ChIP-seq) of H3K27ac in primary human macrophages and foam cells
We report the enhancer landscape in primary human macrophages and foam cells using ChIP-seq for the H3K27ac histone mark CD14+ monocytes were isolated from the blood of 2 healthy male volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stim...
ORGANISM(S): Homo sapiens 
2015-04-08 | E-GEOD-54972 | biostudies-arrayexpress
TranscriptomicsPost-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake
Global gene expression profiles of peripheral blood of 35 to 42 day-old Yorkshire pigs with extremely low (more efficient) and high RFI (less efficient) values from two Iowa State University lines (the low RFI line, n = 15, and the high RFI line, n =16) that were divergently selected for RFI during...
ORGANISM(S): Sus scrofa 
2016-01-15 | E-MTAB-4179 | biostudies-arrayexpress
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