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ProteomicsQuick and clean: Cracking E.coli’s code by LC-MS/MS, de novo sequencing, and dictionary search
In this study, we faced the challenge of deciphering a protein that has been designed and expressed by E.coli in such a way that the amino acid sequence encodes two concatenated English sentences. The sequence carried unknown modifications and cannot be found online. The letters ‘O’ and ‘U’ are both...
ORGANISM(S): Escherichia coli 
2020-05-26 | PXD012015 | Pride
Proteomics E.coli De novo sequencing 
TranscriptomicsGene expression of HCT116 cells after stimulation with oncostatin M (OSM)
To evaluate gene expression profiles in intestinal epithelial cells (IEC) after OSM stimulation, we have employed whole genome microarray expression profiling as a discovery platform to identify relevant genes which are potentially of interest to reveal the role of OSM in intestinal inflammation. T...
ORGANISM(S): Homo sapiens 
2014-12-13 | E-GEOD-53295 | biostudies-arrayexpress
ProteomicsAlphaViz: Visualization and validation of critical proteomics data directly at the raw data level
Although current mass spectrometry (MS)-based proteomics identifies and quantifies thousands of proteins and (modified) peptides, only a minority of them are subjected to in-depth downstream analysis. With the advent of automated processing workflows, biologically or clinically important results wit...
ORGANISM(S): Homo sapiens (Human) 
2022-07-11 | PXD034223 | Pride
Tims Dia-nn Validation Tof Python Quality control Maxquant Open source Data visualization Alphapept 
TranscriptomicsMicroarray Quality Control Study 2, Neuroblastoma one-color
This set of profiles was utilized to construct, validate and evaluate a gene-expression based classifier of outcome of neuroblastoma patients
ORGANISM(S): Homo sapiens 
2010-12-31 | E-MTAB-179 | biostudies-arrayexpress
UnknownGenetic markers of toxicity from capecitabine and other fluorouracil-based regimens: investigation in the QUASAR2 study, systematic review, and meta-analysis.
Not available
S-EPMC4879695 | biostudies-literature
TranscriptomicsTAp73 is a trophic factor essential for sperm cell adhesion and maturation in testis
A core evolutionary function of the p53 family is to protect the genomic integrity of gametes. However, the role of p73 in the male germline is unknown. Here we uncover that TAp73 unexpectedly functions as adhesion and maturation factor of the seminiferous epithelium orchestrating spermiogenesis. TA...
ORGANISM(S): Mus musculus 
2013-12-31 | E-GEOD-46034 | biostudies-arrayexpress
TranscriptomicsTAp73 is essential for germ cell adhesion and maturation in testis
A core evolutionary function of the p53 family is to protect the genomic integrity of gametes. However, the role of p73 in the male germline is unknown. Here we uncover that TAp73 unexpectedly functions as adhesion and maturation factor of the seminiferous epithelium orchestrating spermiogenesis. TA...
ORGANISM(S): Mus musculus 
2014-03-07 | E-GEOD-52124 | biostudies-arrayexpress
TranscriptomicsTranscriptome Sequencing During Mouse Brain Development Identifies Long Non-Coding RNAs Functionally Involved in Neurogenic Commitment
Transcriptome analysis of somatic stem cells and their progeny is fundamental to identify new factors controlling proliferation versus differentiation during tissue formation. Here we generated a combinatorial, fluorescent reporter mouse line to isolate proliferating neural stem cells, differentiati...
ORGANISM(S): Mus musculus 
2013-11-18 | E-GEOD-51606 | biostudies-arrayexpress
TranscriptomicsRNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [microarray]
We generated gene expression profiles from 498 primary neuroblastomas using RNA-Seq and microarrays. We sought to systematically evaluate the capability of RNA deep-sequencing (RNA-Seq)-based classification for clinical endpoint prediction in comparison to microarray-based ones. The neuroblastoma co...
ORGANISM(S): Homo sapiens 
2014-10-21 | E-GEOD-49710 | biostudies-arrayexpress
TranscriptomicsRNA expression data from primary neuroblastoma tumors
RNA expression profiles of 105 primary neuroblastomas derived from customized 4 x 44k oligonucleotide microarrays (Agilent Technologies). These profiles are part of an integrative study combining genomewide epigenetic profiles with transcriptome data of the same neuroblastoma cohort. Tumors were der...
ORGANISM(S): Homo sapiens 
2016-09-08 | E-GEOD-73517 | biostudies-arrayexpress
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