Project description:Based on RNA-seq, we performed transcriptomic profiling to examine the similarities or differences between BICA (bone-in-culture array) and IVBL (in vivo bone lesion). CIBERSORT analysis reveals that the major local cellular components are comparable between BICA and IVBL, but differ dramatically in orthotopic tumors. Principle component analysis of human RNAs indicated that the transcriptomic profiles of cancer cells in BICA are more closely mimicking IVBL, as compared to cancer cells in 2D and in orthotopic tumors. These results provide transcriptome-wide evidence supporting BICA as a platform to mimic bone microenvironment.

2017-01-20 | GSE84114 | GEO

DNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

Project description:Parallel DNA and RNA profiling of EpCAM-positive cells in bone marrow and primary tumor tissue with positive disseminated tumor cell (DTC) count via immunomagnetic Enrichment/Flow Cytometry (IE/FC) of metastatic breast cancer (MBC) patients confirm their malignant nature We developed a novel approach to isolate tumor cells with high purity from bone marrow which was subjected to immunomagnetic enrichment using EpCAM beads followed by fluorescence activated cell sorting (IE/FACS) to isolate EpCAM-positive cells away from leukocytes (CD45+). For DNA profiling, sorted cells were subjected to BAC array comparative genomic hybridization analysis following whole genome amplification. For RNA profiling, QPCR analysis was performed on sixty four (64) cancer-related genes using Taqman® low density arrays. For non-tumor controls, RNA profiling was performed on matched leukocytes (CD45+) isolated from the same enriched bone marrow samples.

2019-04-04 | GSE112756 | GEO

Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease [expression]

Project description:Gene expression profiling of bone marrow-derived mesenchymal stromal cells from healthy donors (n=8), monoclonal gammopathy of undetermined significance (MGUS) (n=10), smoldering myeloma (SMM) (n=10) and multiple myeloma (MM) (n=24) patients. Gene expression profile of MSCs was obtained using high density oligonucleotide microarrays (Human Gene 1.0 ST Array from Affymetrix).

2020-11-25 | GSE137369 | GEO

Profiling in vivo Bone Lesion and ex vivo Bone-In-Culture Array Samples by Next-Generation Sequencing

Project description:Profiling in vivo Bone Lesion and ex vivo Bone-In-Culture Array Samples by Next-Generation Sequencing

| PRJNA328044 | ENA

Primary Human Osteoblasts miRNA array

Project description:A microRNA array was performed using human primary osteoblasts (hOB) obtained from trabecular bone of postmenopausal women after knee replacement due to osteoarthritis in order to determine the miRNAs expressed in these osteoblastic cells.

2015-12-21 | GSE74211 | GEO

Mus musculus

Project description:Transcription profiling of mouse liver by array

| PRJNA240894 | ENA

Global miRNA Expression of Bone Marrow Mesenchymal Stem/Stromal Cells in Fanconi Anemia Patients Before Transplantation and Unpaired Bone Marrow Donors

Project description:Fanconi anemia (FA) is a rare genetic disorder characterized by genomic instability, developmental defects and bone marrow failure. Homeostasis of hematopoietic stem cells (HSCs) in the bone marrow partly relies on their direct or indirect interactions with the mesenchymal stem/stromal cells (MSCs). miRNAs can play a critical role during these interactions. There is no study available so far addressing the miRNA profile of bone marrow (BM-) MSCs in the FA disease state. Non-coding RNA expression profiling was performed in BM-MSCs obtained from Donors, as well as FA patients before bone marrow transplantation (preBMT) using GeneChip miRNA 2.0 array. Quality Control (QC) was performed via Normalized Unscaled Standard Errors (NUSE) and Relative Log Expression (RLE) before further analysis.

2022-09-01 | GSE183226 | GEO

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