Project description:Expression analysis (RNA-seq) and RPPA data (see publication) of head and neck cancer patient-derived xenographs (PDXs) revealed Sox-2 and Cav-1 expression to be biomarker determinants of head and neck cancer patient tumor response to cetuximab (EGFR inhibitor) treatment.
Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.
Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.
Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.
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:We developed MHC1-TIP: an optimized mild acid elution-based immunopeptidomics workflow that leverages data independent acquisition and the Astral mass analyzer to enable scalable, single-tube and cost-effective MHC-I ligandome profiling. This dataset includes immunopeptidomics and proteomics data from the A375 melanoma cell line, colorectal cancer patient-derived organoids, and renal cell carcinoma tumour fragments. We show the effects of TGF-beta treatment on the proteome and immunopeptidome of A375 cells and interferon-gamma treatment on patient-derived organoids. We also explore immunopeptidome and proteome heterogeneity in patient-derived tumour fragments. MB_30: A375 immunopeptidomes in DDA (wildtype and B2M knockout); MB_38: Proteomes with and without mild acid treatment with A375 cells; MB_39: Proteomes and immunopeptidomes from TGFb treated A375 cells; MB_41: MHC1-TIP and MHC-I immunoprecipitation data from different A375 cell input numbers; MB_43: immunopeptidomes of A375 cells treated with different doses of interferon-gamma; MB_45: immunopeptidomes of A375 cells with MHC1-TIP and immunoprecipitation after mild acid elution to identify intracellular peptides; MB_46: Proteomics and immunopeptidomics data from 15 ex-vivo cultured patient-derived tumour fragments; MB_49: Proteomics and immunopeptidomics data from 3 patient-derived organoid lines.
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:We employed ChIP-seq to detect poised and active chromatin regions in cisplatin sensitive and resistant head neck squamous cell carcinoma patient derived primary and lymph node cell lines.