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TranscriptomicsLong Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells
Repair of DNA double-strand breaks (DSBs) by non-homologous end-joining is critical for neural development, and brain cells frequently contain somatic genomic variations that might involve DSB intermediates. We now use an unbiased, high-throughput approach to identify genomic regions harboring recur...
ORGANISM(S): Mus musculus 
2016-02-15 | E-GEOD-74356 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Atlantic salmon fed with a low, medium or high histidine diet
Atlantic salmon at their 2nd year in sea were fed with a low, medium or high histidine diet (L, M, and H, respectively) for several months. Samples were taken at three time points, after the first, second and third period, and a number of fishes were assigned to a new feed group following a crossove...
ORGANISM(S): Salmon salar 
2009-03-27 | E-TABM-678 | biostudies-arrayexpress
TranscriptomicsIdentification of genes expressed during ROL barrier formation in rice root
Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restric...
ORGANISM(S): Oryza sativa 
2014-02-18 | E-GEOD-52128 | biostudies-arrayexpress
ProteomicsGluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes
This study aimed to identify proteolytic fragments of gluten proteins recognized by recombinant IgG1 monoclonal antibodies generated from single IgA plasma cells of celiac disease lesions. Peptides bound by monoclonal antibodies in complex gut-enzyme digests of gluten treated with the deamidating en...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080779 | MassIVE
TranscriptomicsDefault DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (ChIP-chip and MIRA-chip)
To understand what dictates the emerging patterns of de novo DNA methylation, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells using MIRA-chip, ChIP-chip, and strand-specific RNA-seq, respectively. De novo methylation occurred without any apparent tr...
ORGANISM(S): Mus musculus 
2013-07-31 | E-GEOD-45836 | biostudies-arrayexpress
TranscriptomicsComparison of the DNA methylation of bovine blastocysts and bovine sperm
DNA from expanded bovine blastocysts and bovine sperm were extracted then subjected to methylation-sensitive enzymatic digestion and LM-PCR enrichment before being hybridized onto a microarray. Two-condition experiment, bovine blastocysts (pools of 10) vs bovine sperm. Four biological replicates of ...
ORGANISM(S): Bos taurus 
2014-09-09 | E-GEOD-57709 | biostudies-arrayexpress
TranscriptomicsmicroRNA profiling in pediatric AML
MicroRNAs (miRNAs) play a pivotal role in the regulation of hematopoiesis and development of leukemia. Great interest emerged in modulating miRNA expression for therapeutic purposes. In order to identify miRNAs, which specifically suppress leukemic growth of AML with t(8;21), inv(16) or MLL-rearrang...
ORGANISM(S): Homo sapiens 
2014-01-01 | E-GEOD-52541 | biostudies-arrayexpress
TranscriptomicsSystematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in ...
ORGANISM(S): Homo sapiens 
2010-09-30 | E-GEOD-10114 | biostudies-arrayexpress
MetabolomicsUltra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS

Detailed characterization of complex biological surfaces by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) requires instrumentation that is capable of high mass resolving power, mass accuracy and dynamic range. Fourier transform ion cyclotron resonance mass sp...

2022-01-28 | MTBLS3154 | MetaboLights
TranscriptomicsTranscriptomic study of the impact of iron toxicity on rice plant
transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv M-bM-^@M-^XI Kong PaoM-bM-^@M-^Y ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm). Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and...
ORGANISM(S): Oryza sativa 
2012-05-14 | E-GEOD-36299 | biostudies-arrayexpress
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