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TranscriptomicsMismatch oligonucleotides in human and yeast
Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM) structure has not been extensively studied. Here, we present the ...
ORGANISM(S): Homo sapiens 
2010-05-05 | E-GEOD-13175 | biostudies-arrayexpress
TranscriptomicsImmunoregulatory actions of epithelial cell PPAR g at the colonic mucosa
BACKGROUND: Peroxisome proliferator-activated receptor g (PPAR g) is a nuclear receptor whose activation has been shown to modulate macrophage and epithelial cell-mediated inflammation. The objective of this study was to use a systems approach for investigating the mechanism by which the deletion o...
ORGANISM(S): Mus musculus 
2010-07-08 | E-GEOD-20621 | biostudies-arrayexpress
TranscriptomicsLow input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells
In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with Mbo...
ORGANISM(S): Mus musculus 
2018-11-30 | E-MTAB-5875 | biostudies-arrayexpress
UnknownThe Serum Immunoglobulin G Glycosylation Signature of Gastric Cancer.
Not available
S-EPMC4322429 | biostudies-literature
TranscriptomicsTrimming of sequence reads alters RNA-Seq gene expression estimates
Background High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to analyze the resulting data are still immature. One pre-processing step that is widel...
ORGANISM(S): Drosophila melanogaster 
2016-02-25 | E-GEOD-72884 | biostudies-arrayexpress
TranscriptomicsMismatch oligonucleotides in human
Tiled regions surrounding 5 human genes as 36mers, HBG2, TIMP3, SYN3, FLNA, FBX07. The first three of these genes, we tiled with various mismatch oligos in addition to 'perfect match' oligos. Keywords: Mismatch hybridization experiment Tiled perfect match and various designs of mismatch oligonucleo...
ORGANISM(S): Homo sapiens 
2010-05-05 | E-GEOD-13172 | biostudies-arrayexpress
TranscriptomicsChIP-Seq of ES-E14 mouse embryonic stem cells investigating changes in Sall4
Sall4 is a stem cell factor which is important for embryogenesis. We have genetically modified Sall4 in mouse embryonic stem cells to access the preference of Sall4 binding site. There are three different genetic modifications for the ES cells in the form of Sall4 Knockout (KO), Sall4 Zinc Finger Cl...
ORGANISM(S): Mus musculus 
2021-01-05 | E-MTAB-9197 | biostudies-arrayexpress
GenomicsIn situ Hi-C study of chromatin conformation during early Drosophila development
In this experiment we examined higher order chromatin structure during early Drosophila melanogaster development. We performed in situ Hi-C for hand-sorted non-mitotic embryos at nuclear cycle number 12, 13 and 14, and for embryos at 3-4 hours post fertilisation. During this time in development, the...
ORGANISM(S): Drosophila melanogaster 
2017-04-06 | E-MTAB-4918 | biostudies-arrayexpress
TranscriptomicsThe cell envelope stress response mediated by the LiaFSRLm three-component system of Listeria monocytogenes is controlled via the phosphatase activity of the bifunctional histidine kinase LiaSLm
Most members of the phylum Firmicutes harbor a two-component system, LiaSR, which is involved in the response to cell envelope stress elicited most notably by inhibitors of the lipid II cycle. In all LiaSR systems studied in detail LiaSR-mediated signal transduction was shown to be negatively contro...
ORGANISM(S): Listeria monocytogenes EGD-e 
2010-11-16 | E-GEOD-24107 | biostudies-arrayexpress
TranscriptomicsChromatin immunopreciptiation to detect H3K27me3 variations in human gastric cancer samples
H3K27me3 variations were analyzed in 8 pairs of GC and adjacent normal tissues , from 8 GC patients, using chromatin immunoprecipitation linked to microarrays (ChIP-chip) approach. ChIP-real time PCR is used to validate the microrray results. In addition, DNA methylation status also be further analy...
ORGANISM(S): Homo sapiens 
2008-11-30 | E-TABM-594 | biostudies-arrayexpress
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