Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray of peripheral blood mononuclear cells from palindromic rheumatism patients during and between flares.

ABSTRACT: Aim: To assess the gene expression profiles of peripheral blood mononuclear cells obtained from palindromic rheumatism patients during flares and between flares. Samples were paired so we could assess the differences in gene expression profiles per a given patient during a flare and between flares. Method: PBMCs were extracted from whole blood and run on Illumina HT-12 v4 beadchips. The raw data from Illumina’s iScan software were read into R (version 3.4.4) and processed (background corrected, normalised and summarised) using the beadarray package (version 2.34.0). Linear models made using Limma (version 3.34.9) were used to assess differential expression of genes (DEGs).

ORGANISM(S): Homo sapiens

SUBMITTER: Shoaib Ajaib

PROVIDER: E-MTAB-9179 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Molecular, Phenotypic, and Sample-associated Data to Describe Pluripotent Stem Cell Lines and Derivatives

Project description:The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples. Cell lines were differentiated and characterized at a central laboratory using standardized cell culture methodologies, protocols, and metadata descriptors. Stem cell and derived differentiated lines were characterized using RNA-seq, miRNA-seq, copy number arrays, DNA methylation arrays, flow cytometry, and molecular histology. All materials, including raw data, metadata, analysis and processing code, and methodological and provenance documentation are publicly available for re-use and interactive exploration at https://www.synapse.org/pcbc . The goal is to provide data that can improve our ability to robustly and reproducibly use human pluripotent stem cells to understand development and disease. 114 samples This submission represents DNA methylation component of study.

2016-08-20 | E-GEOD-85828 | biostudies-arrayexpress

Human Developmental Biology Resource (HDBR) expression resource-RNAseq

Project description:The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840, this submission) and HDBR expression resource- SNP data (E-MTAB-4843). It is unique in the age range (4 post conception weeks [PCW] to 17PCW) and number of brains studied, particularly those under 8PCW. It is also unique in that both the large-scale data sets and the corresponding RNA and DNA samples are available, the latter via the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR; http://www.hdbr.org). There are 628 RNA-seq datasets from different regions of the brains studied. The number of regions depends on the stage and size of the sample and/or the tissue available. Embryos (4-8PCW) have been staged using a modified Carnegie staging system, details can be found at http://database.hudsen.eu/. All the RNAseq datasets from the same brain have the same embryo/fetus number (e.g. RNAseq datasets HDBR251-HDBR254 are from different tissues from embryo number 1406). The embryo/fetus ID number is recorded in the individual column. The majority of the brains studied are between 4 and 12PCW. During this time the major brain regions are established and there are the early stages of cortex development. DNA was prepared from all the tissues used for RNA-seq analysis and SNP genotype data generated from one tissue from each brain. RNA-seq data and SNP-data from the same tissue and brain have the same name (e.g. HDBR469). There are also SNP genotype data from 229 additional specimens in paraffin wax blocks available for individual gene expression studies. These data are in the accompanying HDBR expression resource- SNP data (E-MTAB-4843).

2016-10-12 | E-MTAB-4840 | biostudies-arrayexpress

Senescent and myofibroblastic cancer-associated fibroblasts share a contractile phenotype regulated by NOX4 generation of reactive oxygen species in the tumour microenvironment

Project description:Cancer associated fibroblasts characterized by an myofibroblastic phenotype play a major role in the tumour microenvironment, being associated with poor prognosis. We found that this cell population is made in part by senescent fibroblasts in vivo. As senescent fibroblasts and myofibroblasts have been shown to share similar tumour promoting functions in vitro we compared the transcriptosomes of these two fibroblast types and performed RNA-seq of human foetal foreskin fibroblasts 2 (HFFF2) treated with 2ng/ml TGF-beta-1 to induce myofibroblast differentiation or 10Gy gamma irradiation to induce senescence. We isolated RNA 7 days upon this treatments changing the medium 3 days before the RNA extraction. A series of SAM alignment files (named after the sample names, for simplicity) are available under http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3101/files/ .

2017-06-01 | E-MTAB-3101 | biostudies-arrayexpress

The ortholog of DDM1 is mainly required for CHG and CG methylation of heterochromatin and is involved in DRM2-mediated CHH methylation that targets mostly genic regions of the rice genome

Project description:OsDDM1 and OsDRM2 display functional specificities that define distinct DNA methylation pathways in the bulk of DNA methylation of the rice genome Cr_DJ.CG.bw: Cr_DJ CG methylation Cr_DJ.CHG.bw: Cr_DJ CHG methylation Cr_DJ.CHH.bw: Cr_DJ CHH methylation ddm1ab.CG.bw: ddm1a/1b CG methylation ddm1ab.CHG.bw: ddm1a/1b CHG methylation ddm1ab.CHH.bw: ddm1a/1b CHH methylation S706.CG.bw: osdrm2 CG methylation S706.CHG.bw: osdrm2 CHG methylation S706.CHH.bw: osdrm2 CHH methylation H3k9me2_macs_peaks.xls: CrDJ H3K9me2 modification peaks H3k9me2_macs_treat_afterfiting.wig: CrDJ H3K9me2 modification wig CrDJ_K27_macs_peaks.xls: CrDJ H3K27me3 modification peaks CrDJ_K27_macs_treat_afterfiting.wig: CrDJ H3K27me3 modification wig DJvsddm1a1b_DESeq2_treated_results.xls: CrDJ and osddm1a1b different expression genes DJvsS706_DEseq2_treated.results.xls: CrDJ and osdrm2 different expression genes smRNA24nt.gff: CrDJ 24nt smRNA smRNA24nt.706.gff: osdrm2 24nt smRNA

2016-06-13 | E-GEOD-81436 | biostudies-arrayexpress

RNA-Seq of WT and Mecp2 KO hippocampus after transplantation with Neural/Precursor Cells (NPCs)

Project description:RTT represents the first genetic cause of severe intellectual disability in girls and although potentially treatable, no cure is currently available. The identification of a valid therapy is delayed by the need of maintaining physiological MeCP2 levels and by the limited comprehension of its roles. Neural precursor cell (NPC) transplantation has already been proved safe and efficacious in many neurological disorders. Particularly, in neurodegenerative conditions, their mechanism of action mainly relies on cell replacement; however, when neurodegeneration is absent, it has been demonstrated that NPCs act by a so-called “bystander” mechanism, by releasing of a plethora of molecules, including inflammatory cytokines, chemokines, trophic factors and stem cell regulators. These factors exert immunomodulatory and neuroprotective effects, and can also modulate synaptic plasticity. Willing to come with a novel cure for RTT, starting from our data indicating the therapeutic potential of NPCs in Mecp2 deficient animals and neurons, we aim at identifying the molecules and/or pathways involved in their therapeutic benefit, a required step for moving the therapy from the bench to the bedside. By bulk RNA sequencing (RNA-seq), we analyzed the transcriptional profile of the hippocampus derived from WT and Mecp2 KO animals, injected with NPCs or vehicle (PBS) at post-natal day (P) 45. Analysis was conducted 20 days after transplantation (at P60). n=5-6 animals/exp.group.

2024-08-27 | E-MTAB-14403 | biostudies-arrayexpress

Microarray gene expression analysis of T-cell prolymphocytic leukemia (T-PLL) patient samples

Project description:T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive neoplasm of mature T-cells with an urgent need for rationally designed therapies to address its notoriously chemo-refractory behavior. To characterize the gene expression profiles, 12 T-PLL MNC samples (>90% tumor cell content) were screened with Illumina gene expression arrays (Human HT‐12 v4 rev.2 Expression Beadchips).

2017-09-08 | E-MTAB-5916 | biostudies-arrayexpress

RNA-Seq of WT and Mecp2 KO cerebellum after transplantation with Neural/Precursor Cells (NPCs)

Project description:RTT represents the first genetic cause of severe intellectual disability in girls and although potentially treatable, no cure is currently available. The identification of a valid therapy is delayed by the need of maintaining physiological MeCP2 levels and by the limited comprehension of its roles. Neural precursor cell (NPC) transplantation has already been proved safe and efficacious in many neurological disorders. Particularly, in neurodegenerative conditions, their mechanism of action mainly relies on cell replacement; however, when neurodegeneration is absent, it has been demonstrated that NPCs act by a so-called “bystander” mechanism, by releasing of a plethora of molecules, including inflammatory cytokines, chemokines, trophic factors and stem cell regulators. These factors exert immunomodulatory and neuroprotective effects, and can also modulate synaptic plasticity. Willing to come with a novel cure for RTT, starting from our data indicating the therapeutic potential of NPCs in Mecp2 deficient animals and neurons, we aim at identifying the molecules and/or pathways involved in their therapeutic benefit, a required step for moving the therapy from the bench to the bedside. By bulk RNA sequencing (RNA-seq), we analyzed the transcriptional profile of the cerebellum derived from WT and Mecp2 KO animals, injected with NPCs or vehicle (PBS) at post-natal day (P) 45. Analysis was conducted 20 days after transplantation (at P60). n=5-6 animals/exp.group.

2024-08-28 | E-MTAB-12813 | biostudies-arrayexpress

Genotyping by array: Human Developmental Biology Resource (HDBR) expression resource of prenatal human brain development-SNP data

Project description:The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840) and HDBR expression resource- SNP data (E-MTAB-4843, this submission). It is unique in the age range (4 post conception weeks [PCW] to 17PCW) and number of brains studied, particularly those under 8PCW. It is also unique in that both the large-scale data sets and the corresponding RNA and DNA samples are available, the latter via the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR; www.hdbr.org). There are 628 RNA-seq datasets from different regions of the brains studied. The number of regions depends on the stage and size of the sample and/or the tissue available. Embryos (4-8PCW) have been staged using a modified Carnegie staging system, details can be found at http://database.hudsen.eu/. All the RNAseq datasets from the same embryo/fetus have the same ID number (e.g. RNAseq datasets HDBR251-HDBR254 are from different tissues from embryo number 1406). The embryo/fetus ID number is recorded in the âindividualâ column. The majority of the brains studied are between 4 and 12PCW. During this time the major brain regions are established and there are the early stages of cortex development. DNA was prepared from all the tissues used for RNA-seq analysis and SNP genotype data generated from one tissue from each brain. RNA-seq data and SNP-data from the same tissue and individual embryo or fetus have the same name (e.g. HDBR469). There are also SNP genotype data from 229 additional specimens in paraffin wax blocks available for individual gene expression studies. For the specimens in wax blocks, the SNP genotype data was generated from DNA from either skin or placenta. The tissues present in the corresponding wax block(s) are given in the biosource type column.

2016-10-12 | E-MTAB-4843 | biostudies-arrayexpress

Genotyping of autosomal recessive type of limb-girdle muscular dystrophies

Project description:26 limb-girdle muscular dystrophy patients from Latvia and 34 patients from Lithuania with clinical symptoms of limb-girdle muscular dystrophies, along with 204 healthy unrelated controls were genotyped for 96 most frequent known limb-girdle muscular dystrophies causing mutations for the region, using VeraCode GoldenGate system. More information can be found in article Robust genotyping tool for autosomal recessive type of limb-girdle muscular dystrophies in BMC Musculoskeletal Disorders by I. Inashkina et al.

2016-04-28 | E-MTAB-4662 | biostudies-arrayexpress

Single-cell RNA sequencing of mouse Naïve State and Epiblast Stem Cell like cells

Project description:scRNA-seq of mouse embryonic stem cells (mESC) derived from four different genetic backgrounds grown in ground state conditions and differentiated towards an epiblast stem cell like (EpiSCL) population.

2020-12-15 | E-MTAB-8844 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data