RNA-seq gene expression of flow cytometry sorted breast cancer stem cell populations
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA782004 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:MMTV-PyMT transgenic FVBN mice spontaneously developed breast tumors. Two tumors were collected as replicate samples, and cells from the dissociated tissue were sorted into 2 cancer stem cell (CSC) populations, along with the remaining non-CSCs. The samples were submitted for RNAseq to generate differential gene expression profiles of the breast tumor CSC populations.
2021-11-21 | GSE189223 | GEO
Project description:Midbrain organoid derived from human induced pluriopotent stem cells a new model of Parkinson's Disease. Organ specific organoids can be used to model many diseases, however little is know about these models. We created a flow cytometry workflow to identify cell types in midbrain organoids. We then selected four populations and sorted these populations: Neurons1(CD24++), Neurons2(CD56++), Astrocytes and Radial Glia, using FACS and the antibody intensity gates defined by our workflow. We then performed scRNAseq on the sorted population and identified cell types within the sorted populations.
2023-03-15 | GSE226890 | GEO
Project description:Tumorigenic breast cancer cells characterized by CD44 expression and low or undetectable CD24 levels (CD44+/CD24-/low) may be resistant to chemotherapy and therefore responsible for cancer relapse. Paired breast cancer core biopsies before and after neoadjuvant chemotherapy or lapatinib were obtained and as single cell suspensions stained using antibodies against CD24, CD44, and lineage markers, and then analyzed by flow cytometry. Mammosphere (MS) formation in culture was compared before and after treatment. Global gene expression differences between cancer cells bearing CD44+/CD24-/low cells and all other sorted cells, and between cancer MS and the primary bulk invasive cancers were analyzed. We report that CD44+/CD24-/low tumorigenic breast cancer cells were intrinsically chemoresistant â chemotherapy led to increased CD44+/CD24-/low cells, increased self-renewal capacity on MS assays, and enhanced tumorigeneicity in immunocompromised SCID/Beige mice. Conversely, in patients with HER2 overexpressing tumors, the EGFR/HER2 tyrosine kinase inhibitor, lapatinib decreased CD44+/CD24-/low cells, with the majority of these patients after conventional therapy achieving pathologic complete response, a validated surrogate marker for long-term survival. Gene transcription pathways that underlie chemoresistant, MS-forming CD44+/CD24-/low cells involve genes belonging to stem cell self-renewal, Wnt signaling, and early development pathways. Experiment Overall Design: Human breast tumor samples were sorted using flow cytometry to select for cells that were CD44+ and CD24-. Gene expression profiles of these cells were compared with profiles of the other sorted cells (CD24+ and CD44-/CD24-). Experiment Overall Design: Core biopsies of primary breast tumors were taken and placed immediately in cold RPMI-1640 supplemented with 10% heat-inactivated newborn calf serum (HINCS, Invitrogen, Carlsbad, CA). Within an hour, the samples were minced and then digested in 10-15 mL of MEGM with 250-300 units/mL collagenase at 370C. The samples were filtered, washed, and then subjected to hypotonic shock to lyse red blood cells. About 106 single cells were re-suspended, incubated for 15 min at 40C with anti-CD44 (APC), anti-CD24 (FITC), and anti-lineage cocktail antibodies (PE-conjugated anti-CD2, CD3, CD10, CD16, CD18, CD31 and CD 140B) (Pharmingen, San Diego, CA) using the manufacturerâs suggested concentrations. The cells were then washed twice, re-suspended with the viability dye propidium iodide, and analyzed using Dako MoFlo flow cytometry. Side- and forward- scatter were used to eliminate debris and cell doublets, and the Lin- cells were further analyzed by CD44 and CD24 markers.
2009-08-22 | E-GEOD-7513 | biostudies-arrayexpress
Project description:flow cytometry sorted photosynthetic picoeukaryotes in freshwater lakes Raw sequence reads
| PRJNA419134 | ENA
Project description:Tumorigenic breast cancer cells characterized by CD44 expression and low or undetectable CD24 levels (CD44+/CD24-/low) may be resistant to chemotherapy and therefore responsible for cancer relapse. Paired breast cancer core biopsies before and after neoadjuvant chemotherapy or lapatinib were obtained and as single cell suspensions stained using antibodies against CD24, CD44, and lineage markers, and then analyzed by flow cytometry. Mammosphere (MS) formation in culture was compared before and after treatment. Global gene expression differences between cancer cells bearing CD44+/CD24-/low cells and all other sorted cells, and between cancer MS and the primary bulk invasive cancers were analyzed. We report that CD44+/CD24-/low tumorigenic breast cancer cells were intrinsically chemoresistant ─ chemotherapy led to increased CD44+/CD24-/low cells, increased self-renewal capacity on MS assays, and enhanced tumorigeneicity in immunocompromised SCID/Beige mice. Conversely, in patients with HER2 overexpressing tumors, the EGFR/HER2 tyrosine kinase inhibitor, lapatinib decreased CD44+/CD24-/low cells, with the majority of these patients after conventional therapy achieving pathologic complete response, a validated surrogate marker for long-term survival. Gene transcription pathways that underlie chemoresistant, MS-forming CD44+/CD24-/low cells involve genes belonging to stem cell self-renewal, Wnt signaling, and early development pathways. Keywords: two group comparison
2009-08-15 | GSE7513 | GEO
Project description:This study was designed to investigate the efficacy of flow cytometry to accurately identify between normal and cancer cells in colon epithelium in humans diagnosed with colorectal cancer.
| 2406350 | ecrin-mdr-crc
Project description:New techniques for single-cell analysis have led to insights into hematopoiesis and the immune system, but the ability of these techniques to cross-validate and reproducibly identify the biological variation in diverse human samples is currently unproven. We therefore performed a comprehensive assessment of human bone marrow cells using both single-cell RNA sequencing and multiparameter flow cytometry from twenty healthy adult human donors across a broad age range. These data characterize variation between healthy donors as well as age-associated changes in cell population frequencies. Direct comparison of techniques revealed discrepancy in the quantification of T lymphocyte and natural killer cell populations. Orthogonal validation of immunophenotyping using mass cytometry demonstrated good correlation with flow cytometry. Technical replicates using single-cell RNA sequencing matched robustly, while biological replicates showed variation. Given the increasing use of single-cell technologies in translational research, this resource serves as an important reference dataset and highlights opportunities for further refinement. [Funding source] Project Number: 1ZIAHL006163-05 Contact PI / Project Leader: HOURIGAN, CHRISTOPHER Title: DETECTION, PREVENTION AND TREATMENT OF ACUTE MYELOID LEUKEMIA (AML) RELAPSE. Awardee Organization: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
2018-09-21 | GSE120221 | GEO
Project description:Genetically engineered mouse glioblastoma tumors were flow cytometry sorted into CD45 positive and CD45 negative populations followed by single cell RNA seq.
2022-04-06 | GSE175851 | GEO
Project description:Characterization of the entire transcriptomic profile of the five major neural progenitor populations of the SVZ, in particular a new population of abundant immature neuroblasts not already described in the literature.
2022-10-15 | E-MTAB-12265 | biostudies-arrayexpress
Project description:Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry
| PRJNA493078 | ENA