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SRP101638
Mus musculus
3 Downloadable Samples
Description
We characterize histone crotonylation in intestinal epithelium-derived cells through Mass spectrometry, ChIp-Seq and RNA-Seq approaches and show that this modification is removed by class I histone deacetylases, HDAC1, 2 and 3. Overall design: RNA-Seq profile from mouse colon epithelium. ChIP-Seq experiments for H3K18crotonylation and H3K4me3 on mouse colon epithelium. ChIP-Seq experiments for H3K18 crotonylation and H3K18 acetylation on HCT116 cell line treated or not with the HDAC inhibitor MS275 (5 µM) for 18h. All the experiments were performed in triplicate.
Publication Title
Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Selection of B cells subjected to hypermutation in germinal centres (GC) during T-dependent (TD) antibody responses yields memory cells and long-lived plasma cells that produce high affinity antibodies biased to foreign antigens rather than self-antigens. GC also form in T-independent (TI) responses to polysaccharide antigens but failed selection results in GC involution and memory cells are not generated. To date there are no markers that allow phenotypic distinction of T-dependent and T-independent germinal centre B cells. We have now compared the global gene expression of GC B cells purified from mice immunized with either TD or TI antigens and identified eighty genes that are differentially expressed in TD GC.
Publication Title
Axon growth and guidance genes identify T-dependent germinal centre B cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 151 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
Background: Moderate weight loss can ameliorate adverse health effects associated with obesity, reflected by an improved adipose tissue (AT) gene expression profile. However, the effect of rate of weight loss on the AT transcriptome is unknown.
Publication Title
Adipose tissue gene expression is differentially regulated with different rates of weight loss in overweight and obese humans.
Sample Metadata Fields
Sex, Specimen part, Treatment, Subject, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- NextSeq 500
Description
RNA-SEQ of mutants B cell for IgH 3''RR and Emu Overall design: CD43- splenic B-cells from wt, Eµ-deficient or 3''RR deficient mice, non stimulated (NS) or stimulated (S) with 5mg/ml LPS.
Publication Title
E<sub>μ</sub> and 3'RR IgH enhancers show hierarchic unilateral dependence in mature B-cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 28 Downloadable Samples
- Affymetrix Genome-Wide Human SNP 6.0 Array (genomewidesnp6), Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Metaplastic breast carcinomas display genomic and transcriptomic heterogeneity [corrected]. .
Sample Metadata Fields
Disease
View Samples- Homo sapiens
- 28 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Expression profiling of metaplastic carcinoma of the breast
Publication Title
Metaplastic breast carcinomas display genomic and transcriptomic heterogeneity [corrected]. .
Sample Metadata Fields
Disease
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much recent attention. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signaling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, one notable exception being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters to tune FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive looks at the complex genetic network that underlies the diversity in the morphologies of yeast colonies.
Publication Title
Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 124 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Polarity defects are a hallmark of most carcinomas. Cells from invasive micropapillary carcinomas (IMPCs) of the breast are characterized by a striking cell polarity inversion and represent a good model for the analysis of polarity abnormalities. We have performed an in-depth investigation of polarity alterations in 24 IMPCs, compared with invasive carcinomas of no special type (ICNST).
Publication Title
LIN7A is a major determinant of cell-polarity defects in breast carcinomas.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 49 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Medullary Breast Carcinoma, a Triple-Negative Breast Cancer Associated with BCLG Overexpression.
Sample Metadata Fields
Disease, Disease stage
View Samples- Homo sapiens
- 49 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Gene expression was compared between medullary breast carcinoma (MBC) and non medullary basal-like breast carcinoma (non-MBC BLC).
Publication Title
Medullary Breast Carcinoma, a Triple-Negative Breast Cancer Associated with BCLG Overexpression.
Sample Metadata Fields
Disease, Disease stage
View Samples