Bulk RNA seq data from radiotherapy-treated glioma-bearing mice
Ontology highlight
ABSTRACT: The experiment goal was to unveil any modulation of the tumor micro-environment in GL261 and SB28 bearing mice following radiation treatment.
Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs), primed pluripotent stem cells (pPSCs) and 1-day Wnt-differentiated cells (dPSCs). Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Single Indexing) - version 1.
Project description:In this study, we address the difference in adult fibroblasts developmentally originating from different germ layers. Closer, we focussed on HOX gene expression and the potential influence of physiological and pathological conditions in postnatal life. Here we specifically focused on fibroblasts from epileptogenic focus, glioblastoma, soft tissue between galea aponeurotica and periost, and metastases to the brain, at the scale of whole genome expression. Fibroblasts were prepared using the fibroblast-specific kit (Fibroblast MicroBeads, Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer´s instructions.
Project description:In this study, we address the difference in adult fibroblasts developmentally originating from different germ layers. Closer, we focussed on HOX gene expression and the potential influence of physiological and pathological conditions in postnatal life. Here we specifically focused on fibroblasts from the adult face = ectomesenchyme origin and upper limb = mesoderm origin. at the scale of whole genome expression. Fibroblasts were prepared... Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs). Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Dual Indexing, UDI12A) - version 2.
Project description:Total RNA-seq of blasts derived 100 adult T-ALL cases, 211 AML cases and 13 mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, CD34+ HSPCs derived from 9 healthy donors are used as a control. 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); EGAD00001011054, EGAD00001007646, EGAD00001007581 (datasets).
Project description:In the Prdm9-driven sterility of Mus m. musculus x Mus m. domesticus hybrids a Prdm9-interacting hybrid sterility gene was mapped in the X-linked Hstx2 locus. Here we show that the Mir465 microRNA gene cluster is the predicted Hstx2 hybrid sterility factor involved in Prdm9 interaction.
Project description:In this experiment we define the transcriptome of the adult mouse skeleton by performing total-RNA transcriptome-sequencing on osteocytes, the critical regulatory cells in bone. Osteocytes from 16 week-old male mice (n=8) were isolated for 4 bone types across the skeleton: the tibia, femur, humerus, and calvaria. All other soft tissues including marrow were removed from samples before sequencing.
Project description:In this in-vitro study, we demonstrate the different effects of exosomes produced by melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of CMM. Both normal and cancer-associated fibroblast were prepared by a)DMEM with 10% EDS (control); b) DMEM with 10% Exosome-depleted serum (EDS) + 10 microg/ml G-361 exosomes (EXO_G361); c) DMEM with 10% EDS + 10 microg/ml exosomes from FBS (EXO_FBS). The cells were cultured for 72 hours. Transcriptome analysis was performed 72 hours after exosome application. Total RNA was isolated using RNeasy Micro Kit (Qiagen).
Project description:This study was designed to investigate the consequences of substrate stiffness on primary brain microvascular endothelial cells (BMECs) in the presence of fluid shear stress (FSS) of 1.7 dyne/cm2. We utilized two gelatin (GEL) substrates of different w/v% (6.5% and 15%) that were crosslinked with microbial transglutaminase resulting in a Young's modulus of 6 kPa and 30 kPa (respectively).
Project description:We employed single-cell RNA sequencing to understand stromal changes in murine melanomas and draining lymph nodes at single cell resolution at different points of tumour development.