11810 results for "cancer rna-seq"

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• Investigating transcriptional changes in rapidly differentiated iPSC-derived neurons (i3Ns) harbouring the SNCA A53T mutation +/- RSL3

  In this study we performed bulk RNA sequencing of a iPSC-derived rapid neuronal model harbouring the Parkinson's disease associated A53T mutation in SNCA. These neurons were subsequently treated with a low dose of RSL3 (300nM) for 6 hours to establish the transcriptional impact of ferroptosis induction in the presence or absence of SNCA A53T mutation.

  Study EGAS50000001536

• Molecular profiling of MBD4-deficient acute myeloid leukaemia

  We describe two cases of MBD4-deficient acute myeloid leukaemia (AML). Clinical samples were used for molecular analysis, including genomic profiling (genome and exomes), methylation analysis (RRBS) and transcriptional profiling (RNA-sequencing). An analysis and methodological description has been published: “MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML” [PMID: 30049810]

  Study EGAS00001002581

• The Berlin (BLN) panel of glioblastoma cell lines: RNAseq of human gliomasphere cell lines and matched parental tumors

  We generated a panel of nine glioma stem-like cell lines under serum-free cell culture conditions from human glioblastoma samples. In addition to clinical annotation, MR imaging and histological characterization of the parental tumor, as well as xenograft studies of tumorigenecity, transcriptomic profiling of tumor/cell line pairs by RNA sequencing has been performed.

  Study EGAS00001001167

• Capture Hi-C on MM

  In situ promoter capture Hi-C on multiple myeloma cell line KMS11 in experimental triplicates. Hi-C libraries were prepared as previously described (Rao et al., 2014, http://dx.doi.org/10.1016/j.cell.2014.11.021). Promoter capture was based on 32,313 biotinylated 120-mer RNA baits (Agilent). Hi-C libraries were sequenced using Illumina HiSeq 2000 technology. The files are in FASTQ format.

  Study EGAS00001002614

• Transcriptome sequencing of myelodysplasia

  Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

  Study EGAS00001002346

• Whole genome and RNA-sequencing in T-cell acute lymphoblastic leukemia

  Dataset includes whole genome and transcriptomic sequencing data from five T-cell acute lymphoblastic leukemia (T-ALL) patients. Whole genome sequencing has performed from both diagnostic (T-ALL sample) and control (remission sample) samples. RNA-sequencing has performed from diagnostic samples. Samples has been taken from the bone marrow or peripheral blood.

  Dataset EGAD00001008658

• Single cell RNA sequencing data in "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"

  This dataset includes a total of 5 single cell RNA sequencing (scRNAseq) data of SARS-CoV-2 infected human alveolar stem cell culture models. Two scRNAseq data were obtained from SARS-CoV-2 infection with MOI of 1.0 (1 for control and 1 for infected case) and the other three were obtained from SARS-CoV-2 infection with MOI of 0.1 in the study entitled "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2". The 10x Chromium Single Cell 3' Reagent kits were used to generate libraries.

  Dataset EGAD00001006242

• RNASeq of bone marrow endothelial cells upon regeneration, (fetal) niche formation, and steady-state.

  Comprehensive transcriptional characterization of bone marrow endothelial cells by RNA sequencing was performed to determine the molecular properties/signatures of endothelium during bone marrow recovery and niche formation. Regenerative bone marrow endothelium was FACS-isolated from bone marrow aspirates of Acute Myeloid Leukemia patients 17 days after receiving chemotherapy (n=3). Niche-forming endothelial cells were FACS-isolated from fetal bones (gestational age 15-20 weeks) (n=3). Healthy adult bone marrow endothelial cells (n=7) were used as steady-state controls. cDNA was prepared using the SMARTer procedure (SMARTer Ultra Low RNA Kit, Clonetech). The provided file type is FASTQ.

  Dataset EGAD00001003904

• Fecal microbiome predicts treatment response after the initiation of semaglutide or empagliflozin uptake

  To investigate the effect of semaglutide and empagliflozin initiation on the gut microbiome of type 2 diabetes patients. In addition, to analyze whether the pre-treatment gut microbiome can predict the treatment efficacy. Gut microbiome fecal samples donated at four timepoints (Baseline, Month 1, Month 3; Month 12) were studied using 16S ribosomal RNA gene sequencing and analysis.

  Study EGAS50000000531

• Transcriptomic profiling of RIRCD patient skeletal muscle, comparing muscle during affected phase to healthy control, and affected patient with and without additional EARS2 mutations.

  Illumina Nextseq total RNA sequencing profiles of skeletal muscle biopsies of 5 affected patients (F3/2M, F4/1F, F5/1M, F2/2F, F2/1M) compared to 6 control (Control040500, Control3509, Control3934, Control3949, Control4994, Control5106) and comparing 3 patients with additional EARS2 mutations (F2/2F, F2/1M, F5/1M) to 2 patients without (F3/2M, F4/1F). Illumina MiSeq total RNA sequencing profiles of skeletal muscle biopsies from patient F3/1M during affected disease phase (4 replicates: F3-1M_Affected_1, F3-1M_Affected_2, F3-1M_Affected_3, F3-1M_Affected_4) compared to recovered phase (F3-1M_Recovered_1, F3-1M_Recovered_2, F3-1M_Recovered_3, F3-1M_Recovered_4).

  Dataset EGAD00001006381