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GSE48804
Danio rerio
11 Downloadable Samples
Affymetrix Zebrafish Genome Array (zebrafish)
Description
Expression microarray of livers from 4 dpf control zebrafish larvae, larvae treated with azacytidine, and ahcy mutant larvae
Publication Title
DNA hypomethylation causes bile duct defects in zebrafish and is a distinguishing feature of infantile biliary atresia.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Mice with the two calcium-stmulated adenylyl cyclase isoforms (AC1 and AC8; DKO mice) knocked-out show conditioned fear memory deficits. We assessed gene expression changes at baseline and several time points after conditioned fear learning to assess transcriptional changes at different stages of learning. Transcriptional changes were assessed in the amydgdala and hippocampus of DKO and wild-type mice.
Publication Title
Temporal and regional regulation of gene expression by calcium-stimulated adenylyl cyclase activity during fear memory.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 20 Downloadable Samples
Illumina HiSeq 3000
Description
Purpose: Parturition is delayed by approximately 12 hours in transgenic mice expressing human corticotropin-releasing hormone (CRH) in placenta. The goal of the study was to identify the pathways in reproductive tissues (uterus and placenta) altered by placental expression of human CRH. Methods: Human BAC RP11-366K18 (CHORI) containing human CRH and cis-regulatory region was inserted into the mouse genome by microinjection and random integration to create the BAC1 line. The CRISPR/Cas9 system was used to delete a CRH regulatory element from the BAC1 line to create the CR1 line, eliminating expression of CRH in placenta. Total expression of uterus and placenta by RNA-seq at embryonic day 18.5 were compared between BAC1, CR1, and nontransgenic mice. Results: Genes known to be associated with luteolysis and initiation of parturition (Cav1, Gja1, Oxtr, Ptgs1, Ptgs2) were not differentially expressed in uterus of this model. Conclusions: CRH-mediated delay of parturition is likely independent of luteolysis. Overall design: mRNA-seq was performed on uterus and placenta harvested at embryonic day 18.5 from nontransgenic mice, Tg(BAC1) mice, and Tg(CR1) mice.
Publication Title
Anthropoid primate-specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 16 Downloadable Samples
- IlluminaHiSeq2000
Description
Objective: Amniotic fluid (AF) is a proximal fluid to the fetus containing higher amounts of cell-free fetal RNA/DNA than maternal serum, thereby making it a promising source for novel biomarker discovery of fetal development and maturation. Our aim was to compare AF transcriptomic profiles at different time points in pregnancy to demonstrate unique genetic signatures that would serve as potential biomarkers indicative of fetal maturation. Methods: We isolated AF RNA from 16 women at different time points in pregnancy: 4 from 18-24 weeks, 6 from 34-36 weeks, and 6 from at 39-40 weeks. RNA-sequencing was performed on cell-free RNA. Gene expression and splicing analyses were performed in conjunction with cell-type and pathway inference. Results: Sample-level analysis at different time points in pregnancy yielded a strong correlation with cell types found in the intrauterine environment and fetal respiratory, digestive and external barrier tissues of the fetus, using high-confidence cellular molecular markers. While some genes and splice variants were present throughout pregnancy, an abundant number of transcripts were uniquely expressed at different time points in pregnancy and associated with distinct fetal co-morbidities (respiratory distress and gavage feeding), indicating fetal immaturity. Conclusions: The AF transcriptome exhibits unique cell- and organ-selective expression patterns at different time points in pregnancy that can potentially identify fetal organ maturity and predict neonatal morbidity. Developing novel biomarkers indicative of the maturation of multiple organ systems can improve upon our current methods of fetal maturity testing which focus solely on the lung, and better inform obstetrical decisions regarding delivery timing. Overall design: RNA-Seq from cell-free was used to idenitfy mRNA transcripts indicative of overall fetal maturity.
Publication Title
Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Organismal function is, to a great extent, determined by interactions among their fundamental building blocks, the cells. In?this work, we studied the cell-cell interactome of fetal placental trophoblast cells and maternal endometrial stromal cells, using single-cell transcriptomics. The placental interface mediates the interaction between two semiallogenic individuals, the mother and the fetus, and is thus the epitome of cell interactions. To study these, we inferred the cell-cell interactome? by assessing the gene expression of receptor-ligand pairs across cell types. Moreover, we find that the expression of G-protein coupled receptors is highly cell-type?specific, implying that ligand-receptor profiles could be a reliable tool for cell type identification. Furthermore, we find that uterine decidual cells represent a cell-cell interaction hub with a relatively large?number of potential incoming and outgoing signals. Decidual cells differentiate from their precursors, the endometrial stromal fibroblasts, during uterine preparation for pregnancy. We show that decidualization (even in vitro) enhances the ability ?to communicate with the fetus, as most of the receptors and ligands up-regulated during decidualization have their counterpart expressed in trophoblast cells. Among the signals transmitted, growth factors and immune signals dominate, suggesting a delicate balance of enhancing and suppressive signals. Finally, this study provides a rich resource of gene ?expression profiles of term intravillous and extravillous trophoblasts, including the transcriptome of the multinucleated syncytiotrophoblast. Overall design: We sequenced mRNA from primary human endometrial stromal fibroblasts and in vitro human decidualized stromal fibroblasts.
Publication Title
Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
We provide the tissue-level human placental transcriptomes from two term uncomplicated pregnancies. Tissue was collected at term C-section (no labor), from villous part of the placenta. Overall design: mRNA-seq of placenta from two term healthy pregnancies.
Publication Title
Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Breast cancer is the most common cancer in women worldwide and metastatic dissemination is the principal factor related to death by this disease. Breast cancer stem cells, are thought to be responsible for metastasis and chemoresistance.. In this study, based on whole transcriptome analysis from putative breast CSCs and reverse-engineering of transcription control networks, we were able to identify two networks associated to this phenotype.
Publication Title
Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype.
Sample Metadata Fields
Age, Disease stage
View Samples- Homo sapiens
- 12 Downloadable Samples
- IlluminaHiSeq1500
Description
During cerebellar development, the main portion of the cerebellar plate neuroepithelium (NE) gives birth to Purkinje cells and interneurons, while the germinal zone at its dorsal edge, called the rhombic lip (RL), generates granule cells and cerebellar nuclei neurons. However, it remains elusive how these components work together to generate the intricate structure of the cerebellar anlage. In this study, we found that a polarized cerebellar anlage structure self-organizes in three-dimensional (3D) human ES cell (hESC) culture. This NE is capable of differentiating into electrophysiologically functional Purkinje cells. The addition of FGF19 promotes spontaneous generation of dorsoventrally polarized NE structures containing cerebellar and basal plates. Furthermore, further addition of SDF1 promoted the generation of stratified cerebellar plate NE with RL-like germinal zones self-forming at the edge. Thus, hESC-derived cerebellar progenitors exhibit substantial self-organizing potential for generating a polarized structure reminiscent of the early human cerebellar anlage at the first trimester. Overall design: Examination of mRNA profile in two different treated human ES cells .
Publication Title
Self-organization of polarized cerebellar tissue in 3D culture of human pluripotent stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 3 Downloadable Samples
- Illumina Genome Analyzer IIx, Illumina HiSeq 2000
Description
The discovery of the small regulatory RNA populations has changed our vision of cellular regulations. Indeed, loaded on Argonaute proteins they formed ribonucleoprotein complexes that target complementary sequences and achieved widespread silencing mechanisms conserved in most eukaryotes. The recent development of deep sequencing approaches highly contributed to their detection. Small RNA isolation form cells and/or tissues remains a crucial stage to generate robust and relevant sequencing data. In 2006, a novel strategy based on anion-exchange chromatography has been purposed as an alternative to the standard size-isolation purification procedure. However, the eventual biases of such a method have been poorly investigated. Moreover, this strategy not only relies on advanced technical skills and expensive material but is time consuming and requires an elevated starting biological material amount. Using bioinformatic comparative analysis of six independent small RNA-sequencing libraries of Drosophila ovaries, we here demonstrate that anion-exchange chromatography purification prior to small RNA extraction unbiasedly enriches datasets in bona fide reads (small regulatory RNA reads) and depletes endogenous contaminants (ribosomal RNAs and degradation products). The resulting increase of sequencing depth provides a major benefit to study rare populations. We then developed a fast and basic manual procedure to purify loaded small non coding RNAs using anion-exchange chromatography at the bench. We validated the efficiency of this new method and used this strategy to purify small RNAs from various tissues and organisms. We moreover determined that our manual purification increases the output of the previously described anion-exchange chromatography procedure. Overall design: Comparison of small regulatory RNA populations obtained after three different small RNA purification procedures
Publication Title
A user-friendly chromatographic method to purify small regulatory RNAs.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer II
Description
The maintenance of genome integrity is an essential trait to the successful transmission of genetic information. In animal germ cells, piRNAs guide PIWI proteins to silence transposable elements (TEs) in order to maintain genome integrity. In insects, most of TE silencing in the germline is achieved by secondary piRNAs that are produced by a feed-forward loop (the ping-pong cycle), which requires the piRNA-directed cleavages of two types of RNAs: mRNAs of functional euchromatic TEs and heterochromatic transcripts that contain defective TE sequences. The first cleavage which initiates such amplification loop remains poorly understood. Taking advantage of the existence of strains that are devoid of functional copies of the LINE-like I-element, we report that in such Drosophila ovaries, the initiation of a ping-pong cycle is achieved only by secondary I-element piRNAs that are produced in the ovary and deposited in the embryonic germline. This unusual secondary piRNA biogenesis, detected in the absence of functional I-element copies, results from the processing of sense and antisense transcripts of several different defective I-elements. Once acquired, for instance after ancestor aging, this capacity to produce heterochromatic-only secondary piRNAs is partially transmitted through generations via maternal piRNAs. Furthermore, such piRNAs acting as ping-pong initiators in a chromatin-independent manner confer to the progeny a high capacity to repress the I-element mobility. Our study explains at the molecular level the basis for epigenetic memory of maternal immunity that protects females from hybrid dysgenesis caused by transposition of paternally inherited functional I-elements. Overall design: Comparison of Drosophila small RNA populations in ovaries and/or eggs from 3-day-old or 25-day-old females.
Publication Title
piRNA-mediated transgenerational inheritance of an acquired trait.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples