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ERP005289
Mus musculus
180 Downloadable Samples
Illumina HiSeq 2500
Description
Mice carrying embryos that were either Pax6fl/fl;Emx1CreER (experimental group) or Pax6fl/+;Emx1CreER (control group) were given tamoxifen on embryonic day 9.5 (E9.5) to induce Pax6 deletion. Embryos were harvested on E13.5, the cerebral cortices were removed and divided into rostral and caudal halves, and total RNA was extracted. Samples from littermates of the same genotype were pooled. Poly-A mRNA was purified and TruSeq RNA-Seq libraries were prepared and sequenced (100 base paired-end; Illumina, HiSeq v3).
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 27 Downloadable Samples
- Illumina HiSeq 2500
Description
Heparan sulphates (HS) are polysaccharides found on all animal cells whose function is regulated by sulphation. One of the roles of HS is to regulate cell signalling pathways which instruct gene expression. In this study we acquired transcriptomes of telencephalic midline tissue from wild-type embryos or mutant embryos lacking specific enzymes, Hs2st or Hs6st1, involved in the addition of sulphate to HS.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 2500
Description
The dorsomedial part of the rostral telencephalon was dissected from E12.5 Emx1Cre;Gli3fl/+ (control) and Emx1Cre;Gli3fl/fl (mutant) mouse embryos. Tissue from three different embryos was pooled and RNA was used for RNAseq.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 251 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Homo sapiens
- 348 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
We aimed to identify the gene network and pathway biology associated with response to vaccine administration by determining genome-wide alterations in host RNA in children
Publication Title
Sex-Differential Non-Vaccine-Specific Immunological Effects of Diphtheria-Tetanus-Pertussis and Measles Vaccination.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 251 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2, TXK) in an independent cohort.
Publication Title
Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 49 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver.
Sample Metadata Fields
Sex, Specimen part, Treatment, Time
View Samples- Homo sapiens
- 130 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Biomarkers of dietary energy restriction in women at increased risk of breast cancer.
Sample Metadata Fields
Sex, Specimen part, Time
View Samples- Homo sapiens
- 18 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
Promoter methylation was assayed in a number of breast cancer and control normal samples along with the effects of 5'-aza-2'-deoxycytidine on breast cancer cell line transcriptomes.
Publication Title
Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 60 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Dietary energy restriction (DER) reduces risk of spontaneous mammary cancer in rodents. In humans, DER in premenopausal years seems to reduce risk of postmenopausal breast cancer. Markers of DER are required to develop acceptable DER regimens for breast cancer prevention. We therefore examined markers of DER in the breast, adipose tissue, and serum. Nineteen overweight or obese women at moderately increased risk of breast cancer (lifetime risk, 1 in 6 to 1 in 3) ages between 35 and 45 were randomly allocated to DER [liquid diet, 3,656 kJ/d (864 kcal/d); n = 10] or asked to continue their normal eating patterns (n = 9) for one menstrual cycle. Biopsies of the breast and abdominal fat were taken before and after the intervention. RNA was extracted from whole tissues and breast epithelium (by laser capture microdissection) and hybridized to Affymetrix GeneChips. Longitudinal plasma and urine samples were collected before and after intervention, and metabolic profiles were generated using gas chromatography-mass spectrometry. DER was associated with significant reductions in weight [-7.0 (+/-2.3) kg] and in alterations of serum biomarkers of breast cancer risk (insulin, leptin, total and low-density lipoprotein cholesterol, and triglycerides). In both abdominal and breast tissues, as well as isolated breast epithelial cells, genes involved in glycolytic and lipid synthesis pathways (including stearoyl-CoA desaturase, fatty acid desaturase, and aldolase C) were significantly down-regulated. We conclude that reduced expressions of genes in the lipid metabolism and glycolytic pathways are detectable in breast tissue following DER, and these may represent targets for DER mimetics as effective chemoprophylactic agents
Publication Title
Biomarkers of dietary energy restriction in women at increased risk of breast cancer.
Sample Metadata Fields
Specimen part, Time
View Samples