Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).
Project description:MicroRNA array data for 144 Mouse lung tissue RNA samples were processed, out of which, 139 passed the visual Quality Control (QC) and data QC. To determine potential signaling pathways involved with MWCNT-associated pathological changes in comparison to asbestos, we determined up- and down-regulated miRNA expression in lung tissue at 1 year post-exposure.
Project description:H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011060 (dataset).
Project description:Obesity can be considered a worldwide epidemic that has become a major threat to the quality of human life at modern society. Understanding the molecular mechanisms that underlie obesity related phenotypes can help to improve treatment options and drug development.
Project description:Despite the widespread adoption of ChIP-seq there is still no consensus on quality assessment metrics. No single published metric can reliably discriminate the success or failure of an experiment, thus hampering objectivity and reproducibility of quality control. We introduce a new framework for ChIP-seq data quality assessment that overcomes the limitation of previous solutions. Our tool called "ChIC" incorporates a novel set of quality control metrics integrated into one single score summarizing the sample quality and a reference compendium with thousands of published ChIP-seq samples, for easier evaluation of new data. This test dataset contain an example of succesfull and non-succesfull ChIP-seq sample for mouse H3K27me3.
Project description:This single-cell RNA-seq dataset profiles clinical fracture-healing tissues from patients with fracture nonunion and normally healed fracture controls. Eight human specimens were initially collected, including five fracture nonunion samples and three normally healed control samples. After quality-control and integration assessment, two nonunion samples (NUBF01 and NUBF03) were excluded from the final integrated analysis because of marked batch-related interference; the final analyzed dataset comprised three nonunion samples (NUBF02, NUBF04, NUBF05) and three control samples (G0531, G0601, G0607). Cell-cell communication analysis prioritized fibroblast-to-osteoblast signaling and highlighted an enhanced LIF-(LIFR+IL6ST) interaction in nonunion tissue.
Project description:Stress-related illness represents a major burden on health and society. Understanding the molecular mechanisms underlying stress responses is an important step to understanding these diseases and designing treatments. Corticotrophs of the anterior pituitary play a central role in the generation of hormonal stress responses, by secreting the stress hormone ACTH in response to stressful stimuli. However, it is poorly understood how they change in response to chronic stress, and whether they return to their original state after the stress has ended. We performed bulk RNA-sequencing of FACS-sorted corticotrophs from male POMC-GFP mice before or after exposure to chronic stress, and after 4 or 12 weeks of recovery, to determine the effect of chronic stress (and of recovery) on corticotrophs transcriptome. This revealed extensive differential gene expression, especially during the recovery period. N.B. Some of the control samples in this dataset (CM1, 2, and 3) are shared with the related experiment, E-MTAB-12885.