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GSE8238
Rattus norvegicus
4 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Follicle assembly is the process by which groups or nests of oocytes break down to form primordial follicles. The size of the primordial follicle pool is the major determinant of the reproductive lifespan of a female. Previously, progesterone (P4) has been shown to inhibit follicle assembly, while tumor necrosis factor alpha (TNF-alpha) has been shown to promote the apoptosis that is necessary for follicle assembly. The current study examines how TNF-alpha and progesterone interact to regulate primordial follicle assembly. Ovaries were collected from newborn rats and placed in organ culture to examine the actions of P4 and TNF-alpha. P4 was found to decrease primordial follicle assembly and increase the percentage of un-assembled oocytes both in vitro and in vivo. TNF-alpha treatment did not change the proportion of assembled follicles in cultured ovaries, but did block the ability of P4 to inhibit follicle assembly. Microarray analysis of the ovarian transcriptome revealed that progesterone treatment of the ovaries altered the expression of 513 genes with 132 only expressed after P4 treatment and 16 only expressed in control ovaries. The majority of genes were up-regulated greater than 2-fold over control, with a small subset of 16 genes down-regulated. Categories of genes affected by P4 are described including a group of extra-cellular signaling factors. The progesterone receptors expressed at the time of follicle assembly included the surface membrane progesterone receptors PGRMC1, PGRMC2 and RDA288. The nuclear genomic P4 receptor was not expressed at appreciable levels. Progesterone increased the expression of several genes (TANK, NFkappaB, Bcl2l1 and Bcl2l2) involved in a signaling pathway that promotes cell survival and inhibits apoptosis. Observations indicate that P4 acts through the surface membrane progesterone receptors to regulate primordial follicle assembly, and that TNF-alpha can over-ride the inhibitory actions of P4 on follicle assembly. A major mechanism involved in the actions of P4 is an increase in cell survival genes and inhibition of the apoptosis pathway. Observations provide insight into the hormonal regulation of primordial follicle assembly and lead to novel approaches to potentially manipulate follicle assembly and reproductive capacity.
Publication Title
Interactions between progesterone and tumor necrosis factor-alpha in the regulation of primordial follicle assembly.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 22 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: The cause of labour initiation has yet to be fully elucidated for human pregnancy. This has hindered attempts to find effective therapies for the prevention of preterm labour, which affects up to 10% of pregnancies in the UK and it is the most dominant cause of perinatal death (75% of all cases). The myometrium of the uterus is where contractions that characterise labour take place, and it is here where changes at the molecular level responsible for triggering labour potential originate from. We used RNA-Seq-based mRNA sequencing technology in an attempt to identify mRNA transcripts that are differentially expressed in the myometrium upon the onset of labour, by comparing the expression profiles of tissues samples that represented non-labour (TNL), early labour (TEaL, = 3 cm cervical dilation) and established labour (TEsL, > 3 cm cervical dilation) states at term (> 37 weeks gestation) pregnancy. Methods: Myometrial biopsies from women undergoing Caesarean section were collected in accordance with the Declaration of Helsinki guidelines, and with approval from the local research ethics committee for Chelsea & Westminster Hospital (London, UK; Ethics No. 10/H0801/45). Informed written consent was obtained from all women who participated. Biopsies were excised from the upper margin of the incision made in the lower segment of the uterus, immediately washed with Dulbecco's phosphate-buffered saline (Sigma) and dissected into pieces approximately measuring 2-3 mm3. For RNA study, biopsies were immersed in RNAlater (Sigma) within 6 minutes after biopsy excision from the uterus and stored at 4°c overnight, before being taken out of RNAlater solution to be frozen for long-term storage at -80°c. For CHIP study, biopsies were snap-frozen in liquid nitrogen and stored at -80°c. All specimens were categorised into four groups according to their labour stages: preterm not in labour (PTNL, n=6), term not in labour (TNL, n=8), term in early labour (TEaL, defined as cervical dilatation <3 cm, n=8) and term in established labour (TEsL, defined as cervical dilatation >3 cm, n=6). For each sample, 60-100 mg of myometrium tissue were extracted in TRIzol (Life Technologies) by mechanical homogenisation in a Precellys 24 bead-based homogeniser using 5 cycles of 5000 rpm for 20 seconds, before chloroform treatment and centrifugation at 4°c. RNA was extracted from the aqueous phase of centrifuged homogenates using the TRIzol Plus RNA Purification kit (Life Technologies) with on-column DNase treatment prior to elution, all according to manufacturer's instructions. Final RNA samples were stored at -80°c. The quantity and quality RNA was measured using a Nanodrop ND-1000 spectrophotometer (LabTech), Qubit fluorimeter (Life Technologies) and Bioanalyser 2100 (Agilent Technologies). Preparation of cDNA libraries was carried out using the TruSeq Stranded mRNA Sample Preparation kit (Illumina), following the high-throughput sample (HT) protocol. The quantity and quality of cDNA libraries were also tested by a Qubit fluorimeter and Bioanalyser 2100. TruSeq Stranded libraries were then multiplexed and sequenced with the average of 42 million DNA fragments per sample (100 bp paired-end reads). Quality control was performed using FastQC software (version 0.11.2). RNA-Seq reads was aligned to the GRCh38 Homo sapiens reference genome downloaded from Ensembl (release 81) with HISAT version 2.0.1 using parameters of --known-splicesite-infile --dta-cufflinks --rna-strandness RF --phred33 –p 4 -q. A list of known splice sites generated from the Ensembl GTF file using an accessory python script included in the HISAT2 package was provided to --known-splicesite-infile, of which HISAT2 will make use to assist the alignment of reads spanning two or more exons. Ensembl annotated a total of 65,989 genes, which includes 20,276 protein coding genes. As one human gene usually contains multiple transcript models, we thus conducted a transcript merging procedure to produce gene level models for expression analysis. Specifically, exons labeled as 'retained_intron' were first excluded, then overlapping interval exons of each gene were merged and a final gene level model was produced in GFF format. Only uniquely mapped (i.e. reads with the tag of NH:i:1) reads were used to produce gene read counts and calculate gene expression levels. The raw read count matrix was normalised with DESeq2 (version 1.6.3). Expression level of each gene in each sample was represented as RPKM (reads per kilobase per million mapped reads). Differentially expressed genes (DEGs) between two groups of samples were identified with DESeq2 (version 1.6.3), edgeR (version 3.8.6) and Cuffdiff (version 2.2.1). For DESeq2 and edgeR, we used the normalised read count matrix as input, and for Cuffdiff, we used the alignment bam files with uniquely mapped reads as input. Raw p-values were adjusted by FDR to produce q-values, and q-value of 0.05 were chosen as the cut-off for statistical significance in DESeq2, edgeR as well as Cuffdiff. Results: 22 RNA samples from three different labour groups were sequenced and an average of 53 million reads were obtained from each sample. More than 97.34% of reads were successfully aligned to GRCh38 reference human genome and the unique concordant pair ratio was greater than 92.39%. In total, 60,593 genes were mapped with the following criteria: (1) at least one RNA-seq read assigned to a gene; (2) we only assign a read to a gene when > 90% of this read falls into the exon regions of this gene. The principal component analysis (PCA) of these 22 samples showed that TNL and TEsL samples formed two distinct clusters whereas the TEaL group featured relatively great internal differences. Nevertheless, half of the samples from TEaL group was clustered with the TNL group and the other half was more separated yet closer to two samples of TEsL group. To determine the transcripts associated with labour, three software packages (DESeq2, EdgeR and Cuffdiff) were used to perform differential expression The transcript with a q value <0.05 in at least two methods was defined as a shared differentially expressed gene (DEG). As a result, 132 and 399 genes were identified comparing TNL with TEaL and TEsL, respectively, whereas no gene was significantly differentially expressed between TEaL and TEsL groups. Due to big differences among individual samples, in this study, the expression fold change (FC) was calculated as the ratio of median reads per kilobase per million mapped reads (RPKMs) with the bigger median RPKM divided by the smaller median RPKM. In order to minimise the noise derived from genes with low expression but high FC, we further filtered gene lists according to the following rational: if the original value of any median RPKM was <1, we artificially turned it into 1 before calculating the FC. Finally, two robust gene lists with an expression FC >1.5 between two groups (TNL vs. TEaL and TNL vs. TEsL) were generated containing 70 and 232 DEGs, respectively. Conclusions: This study, for the first time, identifies differentially expressed genes (DEGs) and pathways that are involved in the myometrial transition from non-labouring to labouring phenotype by using samples from different stages of pregnancy and labour. The DEG lists are generated by subjecting the raw data to three sofware packages (DESeq2, edgeR and Cuffdiff), which makes the yield DEGs more robust. We conclude that some early responsive genes in circadian clock and inflammation pathways are likely to account for the labour onset and no significant changes are found on the transcription level once the labour starts. Overall design: Comparisons made between no labour (TNL, n = 8), early labour (TEaL, n = 8) and established labour (TEsL, n = 6) lower segment myometrial tissue samples, which were collected during Caesarean section (CS) with informed written consent
Publication Title
Myometrial Transcriptional Signatures of Human Parturition.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The aim of this study was to investigate the association of gene expression profiles in subcutaneous adipose tissue with percent of total body weight change in 26 kidney transplant recipients.
Publication Title
Expression levels of obesity-related genes are associated with weight change in kidney transplant recipients.
Sample Metadata Fields
Sex, Race
View Samples- Homo sapiens
- 126 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination.
Sample Metadata Fields
Disease, Disease stage
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
p/CIP binds to many nuclear receptors and plays a major role in hormone dependent transcription of genes. Recently, p/CIP was shown to affect mouse stem cell pluripotency.
Publication Title
Critical components of the pluripotency network are targets for the p300/CBP interacting protein (p/CIP) in embryonic stem cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The objective of this study was to reprogram peripheral blood-derived late-endothelial progenitor cells (EPCs) to a pluripotent state under feeder-free and defined culture conditions. Late-EPCs were retrovirally-transduced with OCT4, SOX2, KLF4, c-MYC, and iPSC colonies were derived in feeder-free and defined media conditions. EPC-iPSCs expressed pluripotent markers, were capable of differentiating to cells from all three germ-layers, and retained a normal karyotype. Transcriptome analyses demonstrated that EPC-iPSCs exhibit a global gene expression profile similar to human embryonic stem cells (hESCs). We have generated iPSCs from late-EPCs under feeder-free conditions. Thus, peripheral blood-derived late-outgrowth EPCs represent an alternative cell source for generating iPSCs.
Publication Title
Feeder-independent derivation of induced-pluripotent stem cells from peripheral blood endothelial progenitor cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
YAP knockdown in HUVEC elicits proliferation and cell cycle preogression defects. YAP deficient cells caused arrest in G1 and defects in S-phase entry. The microarray analysis was conducted to identify potential YAP targets that are involved in HUVEC cell cycle regulation
Publication Title
YAP regulates S-phase entry in endothelial cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 35 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Stem cell fate is governed by the integration of intrinsic and extrinsic positive and negative signals upon inherent transcriptional networks. To identify novel embryonic stem cell (ESC) regulators and assemble transcriptional networks controlling ESC fate, we performed temporal expression microarray analyses of ESCs following the initiation of commitment and integrated these data with known genome-wide transcription factor binding. Effects of forced under- or over-expression of predicted novel regulators, defined as differentially expressed genes with potential binding sites for known regulators of pluripotency, demonstrated greater than 90% correspondence with predicted function, as assessed by functional and high content assays of self-renewal. We next assembled 43 theoretical transcriptional networks in ESCs, 82% (23 out of 28 tested) of which were supported by analysis of genome-wide expression in Oct4 knockdown cells. By using this integrative approach we have, for the first time, formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks.
Publication Title
Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Exercise training improves whole body glucose homeostasis through effects largely attributed to adaptations in skeletal muscle; however, training also affects other tissues including adipose tissue. To determine if exercise-induced adaptations to adipose tissue contribute to training-induced improvements in glucose homeostasis, subcutaneous white adipose tissue (scWAT) from trained or sedentary donor mice was transplanted into the visceral cavity of sedentary recipients. Remarkably, nine days post-transplantation, mice receiving trained scWAT had improved glucose tolerance and enhanced insulin sensitivity compared to mice transplanted with sedentary scWAT or sham-treated mice. Mice transplanted with trained scWAT had increased insulin-stimulated glucose uptake in tibialis anterior and soleus muscles and brown adipose tissue, suggesting that the transplanted scWAT exerted endocrine effects. Furthermore, the deleterious effects of high-fat feeding on glucose tolerance and insulin sensitivity were completely reversed if high-fat fed recipient mice were transplanted with trained scWAT. In additional experiments, voluntary exercise training by wheel running for only 11 days resulted in profound changes in scWAT including increased expression of 1550 genes involved in numerous cellular functions, including metabolism. Exercise training causes adaptations to scWAT that elicit metabolic improvements in other tissues, demonstrating a previously unrecognized role for adipose tissue in the beneficial effects of exercise on systemic glucose homeostasis.
Publication Title
A novel role for subcutaneous adipose tissue in exercise-induced improvements in glucose homeostasis.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 162 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the transcriptome of single pancreatic cells at embryonic day e13.5 Overall design: Single cells mRNA of wild-type mouse pancreata at embryonic day 13.5
Publication Title
Single cell transcriptomic profiling of mouse pancreatic progenitors.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples