Ontology highlight
ABSTRACT:
PROVIDER: PRJNA905430 | ENA |
REPOSITORIES: ENA
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Project description:Gene expression in the human foetal heart for a comparison with cardiomyocytes derived from human pluripotent stem cells. Human foetal heart samples were collected from the individual chambers of the heart at various stages of development. This provided the opportunity to perform gene expression analysis and identify genes involved in the formation of the heart in each of the four chambers and at different stages of development. The dataset can be used to benchmark human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) in terms of their maturation state by comparing it to the foetal heart samples. Two commercially available reference RNA sets are included in the analysis in order to characterize future sets of hPSC-CMs.
2015-07-22 | GSE71148 | GEO
Project description:We examined a set of human breast cancers that were laser-microdissected from archived formalin fixed paraffin embedded (FFPE) tissue. These samples represent an important resource; however, they also represent a challenging aCGH application, as they tend to have significant amounts of noise. Our goal was to use known aberrations within these samples as a benchmark for determining the ability to differentiate between sample noise and real signal. Keywords: aCGH
2007-07-27 | GSE8591 | GEO
Project description:We examined a set of human breast cancers that were laser-microdissected from archived formalin fixed paraffin embedded (FFPE) tissue. These samples represent an important resource; however, they also represent a challenging aCGH application, as they tend to have significant amounts of noise. Our goal was to use known aberrations within these samples as a benchmark for determining the ability to differentiate between sample noise and real signal. Keywords: CGH
2007-07-27 | GSE8598 | GEO
Project description:Gene expression in the human foetal heart for a comparison with cardiomyocytes derived from human pluripotent stem cells. Human foetal heart samples were collected from the individual chambers of the heart at various stages of development. This provided the opportunity to perform gene expression analysis and identify genes involved in the formation of the heart in each of the four chambers and at different stages of development. The dataset can be used to benchmark human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) in terms of their maturation state by comparing it to the foetal heart samples. Two commercially available reference RNA sets are included in the analysis in order to characterize future sets of hPSC-CMs. Microarray experiments were performed on human foetal heart samples from first and second trimester hearts, separated in atria and ventricles.
2015-07-22 | E-GEOD-71148 | biostudies-arrayexpress
Project description:ChIP-seq experiments using low numbers of input cells, scaled down to the point where data quality is unnacceptably compromised, reveals limits of the technique. Two-part ChIPseq study using native chromatin (non-crosslinked) generated with MNase from human CD4+ cells. Part 1: Previously published protocol (Barski et al, 2007, Cell 129:823, hereafter called "Benchmark") used with 2x10e7 cells / ChIP with H3K4me3 antibody, compared to modified method ("new") with decreasing input cell numbers spanning 1000-fold range from 2x10e7 cells / IP to 2x10e4 cells/ IP. Part 2: reproducibility of new method studied using triplicate samples at lowest two cell numbers tested: 1x10e5 and 2x10e4 / ChIP, using H3K4me3 and H3K27me3 antisera.
2012-12-03 | E-GEOD-42147 | biostudies-arrayexpress
Project description:Lymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human LNs in vivo and has been used effectively to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies into this immunologically pivotal environment. Our data provide evidence that LN FNAs contain bone fide LN-resident innate immune populations, with minimal contamination of blood material. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, aided by transcriptomics, identify likely receptor-ligand interactions. This represents the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.
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Project description:Results of an unbiased series of 2833 fresh products of conception samples (in conjunction with maternal blood samples for comparison) that were tested using a 300K Illumina SNP array. we report on the rate and type of whole aneuploidies, UPD, partial aneuploidies, copy number variants found in our series as well as the rate of maternal cell contamination vs. true fetal results. 2833 consecutive fresh products of conception samples and corresponding maternal and/or paternal blood samples were analyzed using a SNP array plus informatics algorithms for the purpose of detecting causal chromosome abnormalities. Hypothesized advantages of using SNP microarray with Parental SupportTM informatics over the traditional standard G-banded karyotyping include: direct testing without need for cell culture, faster turn-around time, low failure rate, the ability to detect or rule out maternal cell contamination (MCC), and the detection of small segmental changes, uniparental disomy (UPD) and parent of origin of any aneuploidies. Results showed a 22% MCC rate. In the 78% of samples with true fetal results, 60% had abnormalities with single aneuploidy being the most common. Separate evaluation of the samples to determine the resolution of the SNP array with informatics showed the ability to detect copy number variations (CNVs) as small as 1 MB or less, with 1.4% of samples revealing a clinically relevant microdeletion or duplication.
2015-07-13 | GSE39332 | GEO
Project description:Modest target sequencing yield improvements using Nanopore adaptive sampling to reduce human DNA contamination from clinical tissue samples
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