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GSE73377
Homo sapiens
11 Downloadable Samples
Affymetrix Human Gene 2.0 ST Array (hugene20st), Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Epigenetics and Preeclampsia: Defining Functional Epimutations in the Preeclamptic Placenta Related to the TGF-β Pathway.
Sample Metadata Fields
Specimen part, Disease, Race
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st), Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Description
Placental Tissue Samples from 36 women (17 normotensive women, denoted with a P, and 19 preeclamptic women, denoted with a Q) were analyzed for differenital methylation
Publication Title
Epigenetics and Preeclampsia: Defining Functional Epimutations in the Preeclamptic Placenta Related to the TGF-β Pathway.
Sample Metadata Fields
Specimen part, Disease, Race
View Samples- Escherichia coli str. k-12 substr. mg1655
- 5 Downloadable Samples
Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired.
Publication Title
Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 21 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Nine cigarette smoke condensates (CSCs) were produced under a standard ISO smoking machine regimen and one was produced by a more intense smoking machine regimen. These CSCs were used to treat primary normal human bronchial epithelial cells for 18 hours.
Publication Title
Effects of 10 cigarette smoke condensates on primary human airway epithelial cells by comparative gene and cytokine expression studies.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 23 Downloadable Samples
NextSeq 500
Description
Histological resolution of the murine pancreas occurs within one week after injury. Whether histological resolution constitutes pancreatic recovery at a molecular level is not known. We performed RNA-sequencing on the recovering pancreas to determine the transcriptomic profile within the histologically recovered pancreas. We show that although there is histological resolution one week after injury in mice, compared to baseline (non-injured pancreas), there are still numerous differentially expressed genes (DEGs) at one and even two weeks after injury. Overall, the findings suggest the actual recovery takes longer than initially thought given the differential transcriptomic profile in the pancreas two weeks after injury compared to the baseline pancreas. There is also the possibility of a novel emerging pancreatic transcriptome upon recovery. Overall design: Acute pancreatitis was induced by caerulein hyperstimulation in both male and female C57BL/6 mice. Total RNA was extracted from the head of the murine pancreas in mice at baseline (non-injured; n=8), day 7 (post-injury; n=8), and day 14 (post-injury; n=7). Total stranded RNA libraries (ribo-depleted) were generated and sequenced on the Illumina NextSeq 500 NGS platform. RNA-seq data was analyzed for differentially expressed genes between baseline and day 7 and between baseline and day 14.
Publication Title
Pancreatic gene expression during recovery after pancreatitis reveals unique transcriptome profiles.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 2500
Description
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MeCP2. RTT is characterized by having apparently normal development until 6-18 months, when a progressive decline in motor and language functions begins and breathing abnormalities and seizures present. Despite intense research, the molecular targets of MeCP2 and their contribution to the disease are unknown. Here we present the first comprehensive and comparative transcriptomic and proteomic analysis in a RTT mouse model. Examining whole cortex tissue in symptomatic males (Mecp2Jae/y) and wild-type littermates, we have identified 391 genes and 465 proteins considered to be significantly altered. We observed an overall poor correlation between global gene and protein expression (Pearson correlation 0.12), yet 35 hits were common to both data sets, with 12 hits not described elsewhere. These 35 hits indicate disrupted cellular metabolism, calcium signaling, protein stability, DNA binding and cytoskeletal cell structure in the RTT cortex. Pathway analysis in both data sets identified biological pathways ubiquitous to multiple cell types as well as cell type specific pathways, underscoring the contributions of multiple central nervous system (CNS) cell populations to the disease pathogenesis. These findings prompted us to compare identified 'hits' to a publicly available database containing CNS cell type specific gene expression. This indicated approximately 32% of differentially expressed (DE) genes and 16% proteins were highly enriched in unique CNS cell types, while the remaining DE genes and proteins were ubiquitously expressed and not ascribable to any unique cell population. Our comparative transcriptome and proteome analysis in the cortex of RTT mice supports previous works indicating widespread CNS dysfunction. Overall design: Wild-type (WT) males were bred with heterozygous Mecp2tm1.1Jae/+ (Jaenisch) female mice. The whole cortex of mutant male mice (Mecp2Jae/y) along with WT littermates were collected after postnatal day 60 (P60+). An n of 4 biological replicates per genotype were used, with WT animals serving as controls. For RNA-Sequencing, 2 technical replicates were run per biological replicate.
Publication Title
RNA sequencing and proteomics approaches reveal novel deficits in the cortex of <i>Mecp2</i>-deficient mice, a model for Rett syndrome.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 117 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), characterized by aneuploidy and poor outcome, is unknown. Here, using complementary genome-wide profiling approaches, we show that hypodiploid ALL comprises two major subtypes that differ in the severity of aneuploidy, transcriptional profile and submicroscopic genetic alterations. Near haploid cases with 24-31 chromosomes frequently harbor alterations targeting receptor tyrosine kinase- and Ras signaling (71%) and IKZF3 (AIOLOS; 13%). In contrast, low hypodiploid ALL cases with 32-39 chromosomes are characterized by TP53 alterations (88%), almost half of which are present in non-tumor cells, and have alterations of IKZF2 (HELIOS; 53%) and RB1 (41%). Both near haploid and low hypodiploid tumors exhibit activation of Ras and PI3K signaling pathways, and are sensitive to PI3K inhibition, indicating that these drugs should be explored as a new therapeutic strategy for this frequently lethal form of leukemia.
Publication Title
The genomic landscape of hypodiploid acute lymphoblastic leukemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 41 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene expression profiling was performed of Pax5 wild type bone marrow subsets from common lymphoid progenitors through to Hardy stage F cells. These cells were obtained by flow sorting of bone marrow.
Publication Title
The genomic landscape of hypodiploid acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Targeted therapies have provided advantages to cancer patients, but these therapies are limited by differential responses and developed resistance.
Publication Title
Activation of the AXL kinase causes resistance to EGFR-targeted therapy in lung cancer.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Macaca mulatta
- 12 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Luteolysis of the corpus luteum (CL) during non-fertile cycles involves a cessation of progesterone (P4) synthesis (functional regression) and subsequent structural remodeling. The molecular processes responsible for initiation of luteal regression in the primate CL are poorly defined. Therefore, a genomic approach was utilized to systematically identify differentially expressed genes in the rhesus macaque CL during spontaneous luteolysis. CL were collected prior to (days 10-11 post-LH surge, mid-late [ML] stage) or during (days 14-16, late stage) functional regression. Based on P4 levels, late stage CL were subdivided into functional late (FL, serum P4 > 1.5 ng/ml) and functionally-regressed late (FRL, serum P4 < 0.5 ng/ml) groups (n=4 CL/group). Total RNA was isolated, labeled and hybridized to Affymetrix genome microarrays that contain elements representing the entire rhesus macaque transcriptome. With the ML stage serving as the baseline, there were 681 differentially expressed transcripts (>2-fold change; p< 0.05) that could be categorized into three primary patterns of expression: 1) increasing from ML through FRL, 2) decreasing from ML through FRL, and 3) increasing ML to FL, followed by a decrease in FRL. Ontology analysis revealed potential mechanisms and pathways associated with functional and/or structural regression of the macaque CL. Quantitative real-time PCR was used to validate microarray expression patterns of 13 genes with the results being consistent between the two methodologies. Protein levels were found to parallel mRNA profiles in 4 of 5 differentially expressed genes analyzed by Western blot. Thus, this database will facilitate the identification of mechanisms involved in primate luteal regression.
Publication Title
Dynamic changes in gene expression that occur during the period of spontaneous functional regression in the rhesus macaque corpus luteum.
Sample Metadata Fields
Sex
View Samples