Dataset Information

E-MTAB-3983

ABSTRACT: Sanger Genomics of Drug Sensitivity in Cancer Project (GDSC) RNA-seq cancer cell line gene expression data

TISSUE(S): Testis, Large Intestine, Brain, Prostate Gland, Lung, Mucosa, Liver, Peripheral Nervous System, Kidney, Uterine Cervix, Ovary, Uterus, Pancreas, Stomach, Gall Bladder, Vulva, Thyroid Gland, Esophagus, Hematopoietic System, Placenta, Musculature, Breast, Skin, Bone, Connective Tissue, Bile Duct, Urinary Bladder, Adrenal Gland

DISEASE(S): Colorectal Adenocarcinoma,Essential Thrombocythemia,Prostate Adenocarcinoma,Not Available,Fibrosarcoma,Askin Tumor,Cervical Small Cell Carcinoma,Eosinophilic Leukemia,Undifferentiated Gallbladder Carcinoma,Gallbladder Adenocarcinoma,Brain Glioma,Acute Leukemia,Squamous Cell Carcinoma,Papillary Lung Adenocarcinoma,Plasma Cell Leukemia,Esophageal Squamous Cell Carcinoma,Bladder Transitional Cell Carcinoma,Diffuse Large B Cell Lymphoma,Squamous Cell Lung Carcinoma,Non-small Cell Lung Adenocarcinoma,Adrenocortical Carcinoma,Medulloblastoma,Squamous Cell Breast Carcinoma,Breast Adenocarcinoma,Synovial Sarcoma,Pancreatic Carcinoma,Lung Carcinoma,Non-small Cell Lung Carcinoma,T-cell Leukemia,Hepatocellular Carcinoma,Ovarian Adenocarcinoma,Glioblastoma Multiforme,Sarcoma,Ovarian Granulosa Tumour,Vulvar Carcinoma,Merkel Cell Carcinoma,Normal,Ovarian Germ Cell Tumour,Histiocytoma,Adrenal Gland Neuroblastoma,Hodgkins Lymphoma,Esophageal Carcinoma,Hairy Cell Leukemia,Esophageal Adenocarcinoma,Cervical Squamous Cell Carcinoma,Atypical Carcinoid Tumor,Chondrosarcoma,Carcinoma,Breast Carcinoma,Benign Prostatic Hyperplasia,Mesothelioma,Ductal Carcinoma,Acute Myelomonocytic Leukemia,Choriocarcinoma,Bone Neoplasm,Large Cell Lung Carcinoma,Thyroid Carcinoma,Ovarian Serous Adenocarcinoma,Renal Cell Carcinoma,Multiple Myeloma,Invasive Lobular Carcinoma,Carcinoid Tumor,Melanoma,Small Cell Lung Carcinoma,Burkitts Lymphoma,Leiomyoma,Pancreatic Adenocarcinoma,Gastric Adenocarcinoma,Rhabdomyosarcoma,Salivary Gland Neoplasm,Anaplastic Astrocytoma,Chronic Myelogenous Leukemia,Cervical Carcinoma,Neuroblastoma,Colorectal Carcinoma,Chordoma,Invasive Ductal Carcinoma,Acute Myeloid Leukemia,Cutaneous T-cell Lymphoma,Osteosarcoma,Ovarian Carcinoma,Acute Lymphoblastic Leukemia,Plasmacytoma,Head And Neck Squamous Cell Carcinoma,Cholangiocarcinoma,Lung Adenocarcinoma,Bladder Carcinoma,Endometrial Adenocarcinoma,Diffuse Large B-cell Lymphoma,Testicular Germ Cell Tumor,Lymphoma,Follicular Thyroid Carcinoma,Glioma,Liposarcoma,Ewing Sarcoma,Vulvar Squamous Cell Carcinoma,B-cell Acute Lymphoblastic Leukemia,Large Cell Immunoblastic Lymphoma,Clear Cell Renal Carcinoma

PROVIDER: E-MTAB-3983 | ExpressionAtlas | 2025-01-23

REPOSITORIES: ExpressionAtlas

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Dataset's files

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			Action	DRS
	E-MTAB-3983-analysis-methods.tsv	Tabular
	E-MTAB-3983-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-3983-coexpressions.tsv.gz	Tabular
	E-MTAB-3983-configuration.xml	Xml
	E-MTAB-3983-factors.xml	Xml

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Project description:The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of 'omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects of the 'omics data integration problem such as the design of multi-omics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells. The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3, and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest. On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different 'omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods. The STATegra experimental design consists of a 6 point time course that captures the differentiation of B3 cells containing Ikaros-ERt2 upon Ikaros induction within a 24 hr period. The process was sampled at 0, 2, 6, 12, 18, and 24 hrs respectively after Ikaros induction by Tamoxifen. As control, B3 cells transfected with an empty vector were treated and sampled in the same way as the inducible line. Eight different 'omic technologies were measured on this system: RNA-seq, miRNA-seq, DNase-seq, RRBS-seq, ChIP-seq, scRNA-seq, Proteomics and Metabolomics. Generally, three biological replicates were obtained per platform and were processed as independent batches. Metabolomics analysis was performed using 4 biological batches (7, 8, 9 and 10) and at times 0, 2, 6, 12, 18 and 24 hrs respectively. Each sample was analyzed using gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS).

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E-MTAB-3983

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