HipSci HumanHT 12v4 Expression BeadChip analysis _open access data for healthy volunteers
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Yasin Memari
PROVIDER: E-MTAB-4057 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national induced pluripotent stem cell (iPS cell) resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the using RNAseq of fibroblasts, peripheral blood mononuclear cells (PBMCs) and induced pluripotent stem cells (iPS cells) generated from the skin biopsies or blood of healthy volunteers. This experiment includes the data and expands the metadata from two obsolete ArrayExpress accessions (E-ERAD-216 and E-ERAD-327) for use in the Expression Atlas. For samples derived from E-ERAD-216 the raw data is stored in the European Genome-Phenome Archive (EGA) and is subject to access control. Data from E-ERAD-327 is stored in the European Nucleotide Archive (ENA) and is publicly available.
2016-06-22 | E-MTAB-4748 | biostudies-arrayexpress
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Raw data files for this study can be accessed from the PRIDE database at EMBL-EBI under accession number PXD003903: http://www.ebi.ac.uk/pride/archive/projects/PXD003903.
2016-06-22 | E-PROT-5 | biostudies-arrayexpress
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Methylation analysis using the Infinium HumanMethylation450 BeadChip on iPS cells generated from skin biopsies from healthy volunteers.
2015-11-16 | E-MTAB-4059 | biostudies-arrayexpress
Project description:The purpose of this study was to characterise iPSC-derived human intestinal epithelial organoids (iPSCo) by comparing these cultures with primary purified intestinal epithelial cells (IEC). Intestinal epithelial organoid (IEO) cultures were derived from at least three different lines of iPSCs, RNA was extracted and gene expression was profiled using RNA-sequencing. We compared these profiles with datasets we have previously derived from purified IEC from mature terminal ileum (TI) and sigmoid colon (SC) as well as human fetal proximal gut (FPG) and fetal distal gut (FDG).
2018-10-22 | E-MTAB-7306 | biostudies-arrayexpress
Project description:The purpose of this study was to characterise iPSC-derived human intestinal epithelial organoids (iPSCo) by comparing these cultures with primary purified intestinal epithelial cells (IEC). Intestinal epithelial organoid (IEO) cultures were derived from at least three different lines of iPSCs, DNA was extracted and gene expression was profiled using Illumina Infinium HumanMethylation450Beadarray. We compared these profiles with datasets we have previously derived from purified IEC from mature terminal ileum (TI) and sigmoid colon (SC) as well as human fetal proximal gut (FPG) and fetal distal gut (FDG).
2018-10-23 | E-MTAB-7289 | biostudies-arrayexpress
Project description:Induced pluripotent stem (iPS) cells have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPS cells generated from different cell types are molecularly and functionally similar. Here, we show that iPS cells obtained from fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPS cells into embryoid bodies and different hematopoietic cells. Our results suggest that low-passage iPS cells retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and altered differentiation capacity. These observations might affect ongoing attempts to use iPS cells for disease modeling and also could be exploited for potential therapeutic applications to enhance differentiation into desired cell lineages. This series consists of triplicated mRNA expression microarray data (Affymetrix mouse gene ST 1.0) for an early passage (passage 4) of mouse iPS cells derived from bone marrow granulocytes, splenic B cells, tail tip fibroblasts, and skeletel muscle precursor cells. iPS cells were generated by infecting somatic mouse cells with lentiviruses expressing Oct4, Sox2, Klf4, and cMyc. Total RNA was isolated from iPS cells at different passages.
2010-07-19 | E-GEOD-22908 | biostudies-arrayexpress
Project description:The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.<br>This experiment contains data of dermal fibroblasts from 3 human individuals, unstimulated, sequenced by 10X Genomics technology. Corresponding data from stimulated cells are found under ArrayExpress accession <a href="/arrayexpress/experiments/E-MTAB-5989">E-MTAB-5989</a>.
2018-07-06 | E-MTAB-5988 | biostudies-arrayexpress
Project description:The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.<br>This experiment contains data of dermal fibroblasts from 3 human individuals, stimulated with dsRNA (poly I:C) for 6 hours, sequenced by 10X Genomics technology. Corresponding data from unstimulated cells are found under ArrayExpress accession <a href="/arrayexpress/experiments/E-MTAB-5988">E-MTAB-5988</a>.
2018-07-06 | E-MTAB-5989 | biostudies-arrayexpress
Project description:We superimposed array comparative genomic hybridization (aCGH) data onto existing expression array profiles (GSE3892) to sift out the pivotal genes underlying the pathogenesis of a well defined series of diffuse large B-cell lymphomas (DLBCL). 280 gained and over-expressed genes were identified, located on chromosomes 1q, 3q, 7, 12p12, 18q and 21q. At the most frequently gained region the oncogene MDMX/MDM4 was concurrently over-expressed, which is a critical regulator of p53 function. In regions of frequent chromosomal loss, 36 genes were concurrently down-regulated, restricted to 6q and 15p. These putative tumor suppressor genes included PERP, MAP3K5, CCNDBP1 and β2M, and loss of 6q was associated with poor clinical outcome. Genes identified and chromosomal regions validated in an independent series of DLBCL patients. Overall design fields: Copy number profiles (array CGH) of a series of 42 Diffuse large B-cell lymphoma patient samples were analyzed a) for frequency of aberrations and b) for impact on gene expression. No duplicate samples or dye-swaps were analyzed. a) Statistical analysis of Array CGH data Calling: Areas of gains and losses and their frequencies throughout the dataset were determined from the Bluefuse ratios within the statistical package â??CGHcallâ?? (van de Wiel et al., 2007). Briefly, after smoothing outliers and median normalization, â??DNAcopyâ?? segmentation (Olshen et al., 2004) was applied within CGHcall, after which a call was assigned to each position on the genome. Within CGHcall the probabilities of the calls were determined per chromosomal arm, and a cellularity correction of 0.75 was applied to each sample because tumor cellularity in all DLBCL is estimated to be maximal 75%, taking into account all stromal, endothelial en infiltrating lymphocytes. After calling, we applied â??CGHregionsâ?? (van de Wiel and van Wieringen 2007) to determine regions of consecutive clones with highly similar calls for all samples. This dimension reduction further increases robustness and statistical power for downstream statistical analyses. Called data were used for all downstream analyses. b) Integration with expression data To integrate called array CGH data with expression array data, the array CGH and expression integration tool, ACE-it (van Wieringen et al., 2006), was used. For ACE-it analysis chromosomal amplifications were included in the gains. ACE-it uses the one-sided Wilcoxon rank sum to test which chromosomal aberrations recurrently affect RNA expression and adjust p-values for multiple testing. Only those clones were taken into account which had at least 20% (9) of the samples in one of the other calling states (gain or loss). Only genes were considered relevant with a false discovery rate of <0.1. References - Olshen AB, Venkatraman ES, Lucito R, Wigler M (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-72. - van de Wiel MA, Kim KI, Vosse SJ, van Wieringen WN, Wilting SM, Ylstra B (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23: 892-4. - van de Wiel MA, van Wieringen WN. CGHregions: dimension reduction for array CGH data with minimal information loss. Cancer Informatics. In press 2007. - van Wieringen WN, Belien JA, Vosse SJ, Achame EM, Ylstra B (2006) ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data. Bioinformatics 22: 1919-20.
2010-06-25 | E-GEOD-5138 | biostudies-arrayexpress
Project description:Gene expression studies of human embryonic stem cells undergoing directed differentiation to endothelial cells to identify key transcriptional changes during differentiation
2013-03-19 | E-MTAB-1510 | biostudies-arrayexpress