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• BLUEPRINT September 2016, ChIPmentation Burkitt Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 3 sample(s) Burkitt Lymphoma from lymph node, on Genome GRCh38. 10 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002939

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - mobile_elements

  Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z

  Dataset EGAD00001001048

• Colorectal Adenoma Gene Screen

  A pilot to establish the feasability of using a custom Agilent targeted pulldown of 110 genes implicated in colorectal tumourigensis to sequence for driver mutations in a set of 30 FFPE colorectal adenomas. If successful, we propose to sequence an additional 350 adenomas as part of a MRC research study in order to define the pattern of driver mutations across the spectrum of pathological subtypes including coventional adenomas, serrated adenomas and hyperplastic polyps

  Dataset EGAD00001001879

• RNA-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011819

• CUT&RUN/ChIP-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011821

• CCA Visium spatial transcriptomics data (4 CCA)

  Visium spatial transcriptomics (10X Genomics) performed on 4 CCA samples. Each sample has two paired-end sequencing runs: the first (I1 & I2) are a pair reading indexes; the second (R1 & R2) are a pair reading inserts, with R1 additionally reading 10X barcodes. For histology images, please contact authors.

  Dataset EGAD00001011997

• Whole exome sequencing of advanced gastric cancer

  To define the cellular characteristics of malignant ascites of advanced gastric cancer patients and search for therapeutic strategies, we obtained 5 malignant ascites and 1 cerebrospinal fluid from five patients with gastric cancer. We analyzed single-cell RNA-seq data of 180 cells from 4 malignant ascites and 1 cerebrospinal fluid metastasis using Fluidigm® C1™ System. Whole exome sequencing data was also generated from blood or tumor tissue.

  Dataset EGAD00001005740

• FASTQ files

  Raw FASTQ files obtained from in situ Hi-C of 16 normal B cells (3 naive B cells, 3 germinal center B cells, 3 plasma cells, and 3 memory B cells, together with a merge file for each subpopulation), 7 chronic lymphocytic leukemias (2 unmutated IGHV and 5 mutated IGHV), and 5 mantle cell lymphomas (2 conventional and 3 leukemic non-nodal).

  Dataset EGAD00001006485

• Valid reads

  Valid reads obtained after analyzing in situ Hi-C data of 16 normal B cells (3 naive B cells, 3 germinal center B cells, 3 plasma cells, and 3 memory B cells, together with a merge file for each subpopulation), 7 chronic lymphocytic leukemias (2 unmutated IGHV and 5 mutated IGHV), and 5 mantle cell lymphomas (2 conventional and 3 leukemic non-nodal).

  Dataset EGAD00001006486

• Somatic whole exome sequencing of a hypermutated gliosarcoma case

  The dataset includes the whole-exome sequencing (WES) of an extramedullary tumor anterior to the spinal cord at T4, which was resected and diagnosed as gliosarcoma. The patient initially diagnosed with a low-grade brain glioma via biopsy, followed by adjuvant radiation and temozolomide treatment. WES was performed using Illumina NovaSeq6000 with 2x100 bp reads. Mean coverage of 152.4x and 230.6x was achieved for normal and tumor, respectively.

  Dataset EGAD00001006816