Hashing (sample multiplexing) of MCF7, PC3, DU145 and MDA-MB-231 cells and nuclei using different hashing methods
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER: Viacheslav Mylka
PROVIDER: E-MTAB-9964 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Altered metabolism is a hallmark of cancer, but little is still known about its regulation. Here we measure transcriptomic, proteomic, phospho-proteomic and fluxomics data in a breast cancer cell-line across three different conditions. Integrating these multiomics data within a genome scale human metabolic model in combination with machine learning we systematically chart the different layers of metabolic regulation in breast cancer, predicting which enzymes and pathways are regulated at which level. We distinguish between two types of reactions, directly or indirectly regulated. Directly-regulated reactions include those whose flux is regulated by transcriptomic alterations (~890) or via proteomic or phospho-proteomics alterations (~140) in the enzymes catalyzing them. Indirectly regulated reactions are those that currently lack evidence for direct regulation in our measurements or predictions (~930). Remarkably, we find that the flux of indirectly regulated reactions is strongly coupled to the flux of the directly regulated ones, uncovering a hierarchical organization of breast cancer metabolism. Furthermore, the predicted indirectly regulated reactions are predominantly bi-directional. Taken together, this architecture may facilitate the formation of stochiometrically consistent flux distributions in response to the varying environmental conditions incurred by the tumor cells. The approach presented lays a conceptual and computational basis for a more complete mapping of metabolic regulation in different cancers with incoming additional data.
2020-05-26 | PXD006449 | Pride
Project description:Comparison of human foreskin fibroblasts with different guide RNA compositions undergoing CRISPRa-mediated reprogramming. Cell samples have been collected at days 4, 8 and 12 of pluripotency induction. Each time point has three conditions with either (1) pluripotent reprogramming factor promoter targeting guides (OMKSL), (2) EEA-motif targeting guides (36bp), or reprorgamming factor promoter and EEA-motif targeting guides (OMKSL+36bp). Control samples have been collected from non-treated foreskin fibroblasts.
2018-06-07 | E-MTAB-6186 | biostudies-arrayexpress
Project description:Sequencing of total RNA and polysomal RNA of two cell lines, MCF7 (tumoral) and MCF10A (non-tumoral) Polysomal and total RNA was prepared from biological triplicates from the two cell lines. For each biological triplicate sub-confluent cell monolyers were lysed to produce cytoplasmic extracts. Half of each extract was fractionated on a sucrose gradient and the polysomal fraction recovered. Polysomal-associated RNA was recovered by Trizol extraction. From the second half of each sample total cyoplasmic RNA was recovered (Trizol extraction).
2015-11-24 | E-GEOD-74232 | biostudies-arrayexpress
Project description:The beta2 integrin subunit (CD18) is thought to regulate gamma delta T cells in vivo. The objective of this study was to determine the gene expression changes mediated by loss of CD18 in lung gamma delta T cells. Single cell RNA sequencing was performed on gamma delta T cells (CD3+ gamma delta TCR+) isolated from the lungs of wild type C57BL/6 mice (N=2) and CD18 knockout (Itgb2-/-) mice (N=1).
2020-08-14 | E-MTAB-8732 | biostudies-arrayexpress
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains fetal liver CITE-seq (surface protein and cytosolic RNA content) data from six biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11613 | biostudies-arrayexpress
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains embryonic liver CITE-seq (surface protein and cytosolic RNA content) data from three biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11618 | biostudies-arrayexpress
Project description:MicroRNA (miRNA/miR) miR526b and miR655 overexpressed tumor cell-free secretions promote breast cancer phenotypes in the tumor microenvironment (TME). However, the mechanisms of miRNA regulating TME have never been investigated. With mass spectrometry analysis of MCF7-miRNA-overexpressed versus miRNA-low MCF7-Mock tumor cell secretomes, we identified 34 novel secretory proteins coded by eight genes YWHAB, TXNDC12, MYL6B, SFN, FN1, PSMB6, PRDX4, and PEA15 those are differentially regulated. We used bioinformatic tools and systems biology approaches to identify these markers’ role in breast cancer. Gene ontology analysis showed that the top functions are related to apoptosis, oxidative stress, membrane transport, and motility, supporting miRNA-induced phenotypes. These secretory markers expression is high in breast tumors, and a strong positive correlation exists between upregulated markers’ mRNA expressions with miRNA cluster expression in luminal A breast tumors. Gene expression of secretome markers is higher in tumor tissues compared to normal samples, and immunohistochemistry data supported gene expression data. Moreover, both up and downregulated marker expressions are associated with breast cancer patient survival. miRNA regulates these marker protein expressions by targeting transcription factors of these genes. Premature miRNA (pri-miR526b and pri-miR655) are established breast cancer blood biomarkers. Here we report novel secretory markers upregulated by miR526b and miR655 (YWHAB, MYL6B, PSMB6, and PEA15) are significantly upregulated in breast cancer patients’ plasma, and are potential breast cancer biomarkers.
2023-05-10 | PXD031771 | Pride
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains CITE-seq data (surface protein and cytosolic RNA content) data from two biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11549 | biostudies-arrayexpress
Project description:We used comparative genomic hybridization (CGH) analysis between Bone metastatic derivatives isolated in vivo and parental cells and focused on genomic changes affecting the expression of potential bone metastasis. Total RNA from biological and technical replicates of parental MCF7 and BoM2 bone metastasis derivatives grown for 48 hours in regular media (see growth protocol). High-molecular DNA was isolated from in vitro cultured MCF7 and BoM2 cells using GeneEluteM-bM-^DM-" Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) following manufactureM-bM-^@M-^Ys instructions.
2014-10-01 | E-GEOD-51237 | biostudies-arrayexpress
Project description:In this paper we demonstrated the potential to flag toxicity issues by utilizing data from exploratory experiments which are typically generated for target evaluation purposes during early drug discovery During drug discovery and development, the early identification of adverse effects is expected to reduce costly late stage failures of candidate drugs. As risk/safety assessment takes place rather late during the development process and due to the limited predictivity of animal models to the human situation, modern unbiased high-dimensional biology read-outs are sought, such as molecular signatures of in vivo response using high-throughput cell-based assays. In this theoretical proof-of-concept we provide findings of an in-depth exploration of a single chemical core structure. Via transcriptional profiling we identified a subset of close analogs which commonly down-regulate tubulin genes across cellular contexts, suggesting possible spindle poison effects. Confirmation via a qualified toxicity assay (in vitro micronucleus test) and the identification of a characteristic aggregate-formation phenotype via exploratory high content imaging validated the inititial findings. SAR analysis triggered the synthesis of a new set of compounds and allowed us to extend the series showing the genotoxic effect. We demonstrate the potential to flag toxicity issues by utilizing data from exploratory experiments which are typically generated for target evaluation purposes during early drug discovery. We share our thoughts on how this approach may be incorporated into drug development strategies. Cells were cultured using standard protocols, seeded in 96 well plate, cultured for 8 hours before treatment with a number of inhouse synthesized compounds. The treatments represent different chemical structures/small molecules that have been synthesized in the context of developing a new drug targeting PDE10A.
2015-12-31 | E-GEOD-70611 | biostudies-arrayexpress