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SRP006212
Mus musculus
2 Downloadable Samples
Illumina HiSeq 2000
Description
The number of transcripts where allelic bias is dependent parent-of-origin was predicted at 100-200 until two recent studies applied RNA-Seq to brain regions from reciprocally crossed inbred mouse strains and identified over a thousand novel imprinted loci, including hundreds present in only males or females. Reanalysis revealed that the vast majority of these novel loci are explained by technical and biological variation of the approach, and are not genuine cases of general or sex-specific parent-of-origin allelic expression. Independent replication projects that, at most, a few dozen novel imprinted transcripts are present in the dataset, in line with previous projections of 100-200 total imprinted transcripts. Overall design: Whole brain transcriptome analysis of E17.5 F1 embryos from reciprocally crossed C57BL/6J and CastEi/J parents
Publication Title
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 4000
Description
During early development, pluripotent cells of the epiblast show extensive rewiring of enhancers with little associated change in gene expression. The mechanisms underlying and purpose of this rewiring are largely unknown. Here we identified a transcription factor, GRHL2, that is both necessary and sufficient to activate latent enhancers during the transition from naïve embryonic stem cells (ESC) to primed epiblast cells (EpiC). GRHL2 is necessary to maintain expression of its targets in EpiCs. However, these genes are already expressed at equivalent levels in ESCs, suggesting these genes switch enhancer usage during the transition. Identification of alternative enhancers driving these genes in ESCs uncovered an enrichment for the ESC-specific KLF transcription factors. While many KLF targets remain expressed in EpiCs, GRHL2 only regulates a specific subset promoting an epithelial program. These data suggest a model where a large naïve-specific transcriptional network is partitioned into smaller networks to uncouple their regulation in EpiCs, providing more flexibility in gene regulation during lineage specification. Overall design: RNA-seq in wildtype embryonic stem cells (ESCs) and wildtype epiblast-like cells (EpiLCs)
Publication Title
GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Rattus norvegicus
- 38 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.
Sample Metadata Fields
Sex, Specimen part
View Samples- Rattus norvegicus
- 24 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture, Methotrexate, Isofluorane anesthetic and placebo treatments, as well as the healthy control.
Publication Title
Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.
Sample Metadata Fields
Sex, Specimen part
View Samples- Rattus norvegicus
- 19 Downloadable Samples
- Illumina HiSeq 2000
Description
We report the application of Illumina Hiseq2000 sequencing technology for high-throughput miRNA profiling of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture and placebo treatments. Overall design: The experiment is designed as 2 arms: epidermal needle manipulation (AP/MEC) and placebo (PLA, used as control) on CIA induced rheumatoid arthritis (RA) rats. Muscle tissue samples sampling was carried out before any therapy in RA rats (RA_T0), and after at 1 hour and 34 days of therapeutic treatments for both AP and PLA. From all the 10 blood collected samples (2 replicates for each group, for each timepoint), total RNA were extracted. Finally, purified RNA were analyzed using illumina hiseq 2000).
Publication Title
Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 14 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture and Methotrexate+acupuncture treatment, as well as epidermal needle manipulation on healthy rat model.
Publication Title
Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.
Sample Metadata Fields
Sex, Specimen part
View Samples- Oryza sativa indica group
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Background In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed at progressive stages of development by using microarray and sequence by synthesis technologies to identify genes that regulate anther development. Here we have carried out a comprehensive analysis of rice anther transcriptomes at four distinct stages of development with a focus to identify regulatory components contributing to male meiosis and germline development. Further, these transcriptomes have been compared with transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. Results - To understand the molecular processes that lead to male gametophyte development, transcriptome profiling of four stages of anther development in rice [pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA)] was conducted. Around 22,000 genes were found to be expressed in at least one of the anther developmental stages, with the highest number in MA (18,090) and lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of1,000 genes that are specifically expressed in anther stages. Of them the expression of 453 genes was found to be specific to TPA, whereas 78 and 184 genes were expressed specifically in MA and SCP. Gene ontology and pathway analysis of specifically expressed genes revealed that transcription factors and protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. Conclusions - These data not only provide the transcriptome constituents of four landmark stages of anther development but also identify genes that express exclusively in these stages and therefore may contribute to specific aspects of anther and/or male gametophyte development in rice. Moreover, these gene sets assist in building a deeper understanding of underlying regulatory networks and in selecting candidates for gene function validation.
Publication Title
Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
We report the application of Illumina Hiseq2000 sequencing technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA) and treated with acupuncture or not. Overall design: 2 rats in total, i.e., 2 replicates RA rat model before treatment (RA1, 2) for 3 in vitro culture conditions (standard serum FBS, blood serum from animals acupuncture treated AP+, blood serum from animals acupuncture untreated AP-).
Publication Title
Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 49 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Gene expression patterns related to osteogenic differentiation of bone marrow-derived mesenchymal stem cells during ex vivo expansion.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of this study was to describe the gene expression patterns related to the differentiation and mineralization of bone-forming cells, including activation and/or repression of osteogenic or non-osteogenic pathways, remodeling of cell architecture, cell adhesion, cell communication, and assembly of extracellular matrix. The study implied patient selection, tissue collection, isolation and culture of human marrow stromal cells (hMSC) and osteoblasts (hOB), and characterization of bone-forming cells. RNA samples were collected at defined time points, in order to understand the regulation of gene expression during the processes of cell differentiation/mineralization that occur during bone repair. Transcriptome analysis was performed by using the Affymetrix GeneChip microarray technology platform and GeneChip Human Genome U133 Plus 2.0 Array. Our results help to design a gene expression profile of bone-forming cells during specific steps of osteogenic differentiation. These findings offer an useful tool to monitor the behaviour of osteogenic precursors cultured in presence of exogenous stimuli, i.e. growth factors, or onto 3D scaffolds for bone engineering. Moreover, they can contribute to identify and clarify the role of new genes for a better understanding of the molecular mechanisms regulating osteogenesis.
Publication Title
Gene expression patterns related to osteogenic differentiation of bone marrow-derived mesenchymal stem cells during ex vivo expansion.
Sample Metadata Fields
No sample metadata fields
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