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ProteomicsChemical and Random Additive Noise Elimination (CRANE) - case_study - multicenter_dataset
The effectiveness of the novel electrospray ionisation - liquid chromatography mass spectrometry (ESI-LC-MS) data de-noising technique, CRANE, is demonstrated by denoising the MS1 and all the MS2 windows of the multicentre, data-independent acquisi-tion (DIA) MS dataset from Navarro, et al. (2016).
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2021-07-26 | PXD020529 | Pride
Lc-msms Random noise Chemical noise Denoise Baseline noise Dia 
TranscriptomicsTranscription profiling of rat 3Y1 embryonic fibroblasts to identify MUC1-induced transcriptional alterations
The MUC1 oncoprotein is aberrantly overexpressed in diverse human malignancies including breast and lung cancer. Although MUC1 modulates the activity of several transcription factors, there is no information regarding the effects of MUC1 on global gene expression patterns and the potential role of M...
ORGANISM(S): Rattus norvegicus 
2009-04-19 | E-GEOD-14337 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human CD4+ T-cells and GM6990 lymphoblastoid cell lines
CD4+ T-cells isolated from three normal individuals and GM6990 cell lines (three biological replicates) are compared Experiment Overall Design: 8 arrays comparing CD4+ T-cells and GM6990 lymphoblastoid cell lines
ORGANISM(S): Homo sapiens 
2008-06-13 | E-GEOD-4406 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of brain and spleen from rhesus macaque to validate two oligonucleotide array
We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 hum...
ORGANISM(S): Macaca mulatta 
2007-01-10 | E-TABM-189 | biostudies-arrayexpress
ProteomicsDeletion of Allele-Specific HLAs (DASH)
Evaluting HLA loss of heterozygosity, a key immune escape mechanism, using NGS and immunopeptidomics.
ORGANISM(S): Homo sapiens (Human) 
2021-11-04 | PXD022323 | Pride
Tmt Immunopeptidomics Hla-loh 
TranscriptomicsHigh-throughput gene expression profiling of Salmonella enterica serovar Paratyphi A in the blood of bacteremic patients in Bangladesh
In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh. In total, we detected 1798 S. Paratyphi A mRNA...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Paratyphi A 
2010-09-06 | E-GEOD-22958 | biostudies-arrayexpress
TranscriptomicsFyn-dependent prefrontal cortex gene networks in acute ethanol sensitivity
Fyn kinase has been implicated in multiple behavioral responses to ethanol and in the regulation of myelin gene expression. Here we tested whether Fyn kinase modulated basal or ethanol-responsive expression of genes regulated by acute ethanol in brain regions of the mesolimbocortical dopamine pathwa...
ORGANISM(S): Mus musculus 
2014-08-31 | E-GEOD-49028 | biostudies-arrayexpress
TranscriptomicsIn vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh
We applied an RNA capture and amplification technique, Selective Capture of Transcribed Sequences (SCOTS), and microarray hybridization to identify S. Typhi transcripts expressed in the blood of five humans infected with S. Typhi in Bangladesh. In total, we detected the expression of mRNAs for 2046...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhi 
2011-07-12 | E-GEOD-30565 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of brain and gut neurospheres of wild type and Bmi-1 knockout mice to reveal that Bmi-1 dependence distinguishes neural stem cell self-renewal from progenitor proliferation.
The cRNA derived from Brain and Gut neurospheres of wild type and BMI-1 knockout mice were hybridized to Affymetrix mouse ver 2 Chips A, B and C. In case of brain neurospheres, the cRNA were generated by one round RNA amplification (conventional method). In contrast, the cRNA of Gut neurospheres wer...
ORGANISM(S): Mus musculus 
2007-12-15 | E-GEOD-611 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Arabidopsis treated with sugars (glucose, mannose) and abcissic acid
The aim of the experiment is to determine sugar and ABA responsive gene expression in Arabidopsis.
ORGANISM(S): Arabidopsis thaliana 
2005-10-01 | E-MEXP-475 | biostudies-arrayexpress
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