MRNA-Seq of placentas bearing the OgtY851A mutation
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Mus musculus
SUBMITTER: Charles Girardot
PROVIDER: E-MTAB-13299 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:To understand the underlying cause and mechanisms of embryonic lethality observed in combined loss of E2f7 and E2f8, we compared global gene expression profiles of wild type, germline deleted and sox2-Cre/Cyp19-Cre deleted embryos and placentas. RNA was extracted from E10.5 embryos and placentas. Gene deletion in samples confirmed by PCR genotyping of DNA isolated from each sample.
2012-08-31 | E-GEOD-30488 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes between placentas from pregnancies with PE and placentas from normal pregnancies to search for the candiadate genes for further DNA methylation analysis The differentially expressed genes LEP and SH3PXD2A were further analyzed by DNA methylation. 5 placentas from pregnancies with PE and 7 from normal subjects were included in the gene expression microarray analysis.
2013-02-01 | E-GEOD-43942 | biostudies-arrayexpress
Project description:Shh signal mediated by Gli family of transcription factors regulates digit growth and patterning in early limb development. Shh expression in the posterior margin of the limb bud defines the zone of polarizing activity. However, much less is know about downstream targets that mediate Shh signal functions. In this dataset, we include the expression data obtained from dissected anterior and posterior halves of mouse limb bud respectively. These data are used to obtain 889 transcripts that were upregulated 1.3 fold or more in the posterior limb bud, and 1189 transcripts that were enriched in the anterior limb bud at 1.3 fold or more. Two samples were analyzed. We generate pairwise comparisons between anterior and posterior limb tissues. Genes with a fold-change ≥1.3 were selected.
2013-01-06 | E-GEOD-41691 | biostudies-arrayexpress
Project description:To study function of Embigin in mouse embryos, five E17.5 WT and Emb-/- placentas and lungs were dissected, and the RNA was isolated and submitted to high-throughput sequencing to find differentially expressed genes between WT and Emb knock-out mouse lungs or placentas
2023-08-31 | E-MTAB-10641 | biostudies-arrayexpress
Project description:The proteomes of placentas corresponding to EpoR+/+ and EpoR-/- mice were analyzed by label-free LC-MS/MS.
2022-09-28 | PXD008368 | Pride
Project description:40-PE Smart-Seq of RNA isolated from single 2-cell embryos, single morulae, single blastocysts, single E7 embryos epiblast halves and single E7 trophectoderm halves. For all preimplantation stages, embryos were grown ex-vivo from three experimental groups of zygotes: zygotes injected with the mRNA of a recombinant OGA (named BtGH84) (Btgh_injected), zygotes injected with a catalytically dead version of BtGH84 (dBtgh_injected) (control nr.1) and non-injected zygotes (non_injected) (control nr.2). Postimplantation E7 embryos were grown from two experimental group of zygotes: Btgh-injected and dBtgh-injected (control) and transferred at the 2-cell stage to foster mothers. All samples from the same embryonic stage were processed for single embryo (or single-embryo single-tissue) Smart-Seq library preparation at the same time and then sequenced in the same NextSeq500 run. The different embryonic stages were processed on different days and sequenced in different NextSeq500 runs. Together with the raw fastq files, the table of gene counts obtained with featureCounts is provided, containing all samples that passed filtering steps and were input to the PCA and differential expression analysis (last column of Table S3 of the manuscript).
2024-03-30 | E-MTAB-12981 | biostudies-arrayexpress
Project description:Preeclampsia (PE) is a major contributor of maternal mortality with uncertain etiology. Recent studies suggested that epigenetic modifications, including DNA methylation, play a vital role in the development of PE. In this study, we have mapped genome-wide distribution of 5-methylcytosin (5-mC) and 5-hydroxymethylcytosine (5-hmC) using MeDIP and (h)MeDIP in the placentas from severely preeclamptic patients and normal controls. A total 194485 pooled 5-mC peaks and 138133 pooled 5-hmC peaks were identified, of which 714 5-mC peaks and 119 5-hmC peaks showed significant difference between patients and controls (>2-fold, p<0.05).To our knowledge, this is the first report of DHMRs (Differentially Hydroxy-Methylated Regions) in preeclamptic placenta. We not only confirmed the aberrant DNA methylated regions in the process of preeclampsia reported previously, but also identified unreported regions. A total of 4 selected DMRs (Differentially Methylated Regions) were also confirmed by MassARRAY EppiTYPER. Of these, PTPRN2, which had low level of 5-mC and high level of 5-hmC at gene body, was further verified to have lower methylation level at promoter regions in case group compared with controls. In conclusion, our study provided genome-wide distribution of 5-mC and 5-hmC in severe PE and normal controls, which have further clinical value for the identification of diagnostic and therapeutic markers for severe PE. Examination of 5-mC and 5-hmC pattern in 4 control cases' tissue and 4 severely Preeclamptic Placentas cases' tissue.
2014-12-13 | E-GEOD-63743 | biostudies-arrayexpress
Project description:The RNA-seq experiment was designed to determine the effects of blastocyst transfer on the transcriptome of whole placentas at embryonic day (E) 10.5. C57Bl/6 blastocysts that were from natural matings without superovulation were transferred into the uteri of pseudopregnant B6D2F1 females (at gestational day 2.5 equivalent). RNA libraries were prepared from whole male placentas at E10.5 (N = 4 placentas) from the transfer group alongside RNA libraries from control placentas from C57Bl/6 conceptuses derived from natural matings and did not undergo the transfer process (N = 4 placentas). Libraries were muliplexed and pooled for sequencing on the Illumina NextSeq500 platform with 75-base-pair single-end reads. Sequencing was performed in duplicate to provide at least 18 million reads per sample, and 1% PhiX Control (Illumina) spike-in was used. Quality control of Fastq files was performed using FastQC and fastq_screen. Sequences were trimmed with Trim Galore!, and alinged to GRCm38 mouse genome using STAR aligner.Alignments were processed using custom ClusterFlow (v0.5dev) pipelines and assessed using MultiQC (0.9.dev0). Gene quantification was determined with HTSeq-Counts (v0.6.1p1). Additional quality control was performed with rRNA and mtRNA counts script, feature counts (v 1.5.0-p2) and qualimap (v2.2). Differential gene expression was performed with DESeq2 package (v1.16.1, R v3.4.0). Read counts were normalised on the estimated size factors.
2019-12-31 | E-MTAB-8036 | biostudies-arrayexpress
Project description:Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription. Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling. The genomic expression values of each sample are then measured with oligonucleotide arrays. From this data, genes regulated by organizer signaling are selected and then clustered by their patterns of regulation. A new GO biological process annotation of the Xenopus genome allows us to rapidly identify clusters that are highly enriched for known gastrula patterning genes. Within these clusters, we can predict the expression patterns of unknown genes with remarkable accuracy, leading to the discovery of new organizer-related gastrula stage expression patterns for 19 genes. Moreover, the patterns of gene response observed within these clusters allow us to parse apart the contributions of BMP and Wnt inhibition in organizer function. We find that the majority of gastrula patterning genes respond transcriptionally to these activities according to only a few stereotyped patterns, allowing us to describe suites of genes that are likely to share similar regulatory mechanisms. These suites of genes demonstrate a mechanism where BMP inhibition initiates the organizer program before gastrulation, and Wnt inhibition maintains and drives the organizer program during gastrulation. Experiment Overall Design: In order to describe and separate the genomic expression changes induced by the two main organizing activities, BMP inhibition and Wnt inhibition, we created a panel of gastrula stage ventral tissues that ectopically overexpressed one or both of these activities, and compared these samples to endogenous dorsal and ventral gastrula stage tissue. Two well-studied organizer secreted factors, Noggin and Dickkopf-1 (Dkk-1), were used to ectopically inhibit BMP and Wnt signaling, respectively. Four different overexpression mixtures were injected ventrally into 4-cell embryos: noggin and eGFP (anti-BMP); noggin, dkk-1, and eGFP (anti-BMP and anti-Wnt); dkk-1 and eGFP (anti-Wnt); and eGFP alone. eGFP mRNA was used to trace targeting. Plasmid DNA was used for noggin and dkk-1 overexpression, instead of mRNA, in order to limit ectopic expression of these genes to post-MBT stages, more closely mimicking the endogenous regulation of these genes. The ventrally injected embryos were grown to early stage 10, sorted for appropriately targeted eGFP florescence, and then bisected between the dorsal and ventral halves at either stage 10 (early gastrula) or stage 11.5 (late gastrula). For the noggin and/or dkk-1 injected embryos, only the ventral halves of the embryos were saved, eliminating endogenous organizer tissues. For the embryos injected with only eGFP, both the ventral and dorsal halves were saved, creating separate ventral and dorsal control conditions. These five conditions were each generated twice at both stage 10 and 11.5, with each set of five samples coming from a single clutch of embryos, creating twenty total tissue samples from 4 different clutches. For each batch of injections some sorted embryos were allowed to develop through tailbud stages in order to validate the phenotypes induced by our constructs. Total RNA was then isolated from the twenty tissue samples and applied to Affymetrix oligonucleotide arrays.
2007-10-05 | E-GEOD-3368 | biostudies-arrayexpress
Project description:STOX1A overexpression in mice placenta triggers a preeclamptic phenotype in the mothers, with hypertension, proteinuria and kidney alterations (Doridot et al, Hypertension, 2013), this being connected with NO depletion and increase of nutrosative stress (Doridot et al, Antiox Redox Signal, 2014). Tetrahydrobiopterin (BH4) is a cofactor essential for NO production. We treated preeclamptic mice with this drug, and analyzed placental gene expression in four groups (Control mice, Control mice with BH4, Preeclamptic mice and preeclamptic mice with BH4).
2021-05-01 | E-MTAB-9314 | biostudies-arrayexpress