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• Chronic lymphocytic leukemia IGHV somatic hypermutation detection by targeted capture next-generation sequencing

  FASTQ and BAM files for 46 samples (consisting of 35 samples for patients diagnosed with CLL, 5 samples consisting of a dilution series of patient DNA, and 6 samples of cell lines and dilutions involving the cell lines) from targeted capture next-generation sequencing from the LySeq panel. Libraries were sequenced on either Illumina HiSeq 2500 (LySeq66 PoP, R1-3) or Illumina NovaSeq 6000 (LySeq66 Validation Round).

  Dataset EGAD00001009828

• BLUEPRINT release August 2016, Bisulfite-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh38

  Bisulfite-Seq data for 6 CD14-positive, CD16-negative classical monocyte sample(s). 86 run(s), 6 experiment(s), 12 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002523

• BLUEPRINT release August 2016, Bisulfite-Seq for endothelial cell of umbilical vein (resting), on genome GRCh38

  Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 35 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002294

• BLUEPRINT release August 2016, Bisulfite-Seq for CD3-negative, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  Bisulfite-Seq data for 2 CD3-negative, CD4-positive, CD8-positive, double positive thymocyte sample(s). 29 run(s), 2 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002464

• shallow WGS of cell free DNA

  12.5 ng of cfDNA was used as input for shallow whole-genome sequencing (sWGS), aiming for a coverage of x0.2-0.4-fold. Library preparation was performed using the TruSeq Nano DNA High Throughput Library Prep Kit (Illumina, San Diego, CA, USA) on an automated Hamilton STAR liquid handling system (Hamilton, Germany GmbH, Robotics, Gräfeling, Germany) with dual indexing, and sequencing was performed on the NextSeq500/550 platform (Illumina). The fraction of tumor-derived DNA in cell-free DNA was estimated using the R package ichorCNA.

  Dataset EGAD00001009796

• BLUEPRINT release August 2016, ChIP-Seq for plasma cell, on genome GRCh38

  ChIP-Seq data for 5 plasma cell sample(s). 24 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002281

• Enhanced Detection of Landmark Minimal Residual Disease in Lung Cancer using Cell-Free DNA Fragmentomics

  The circulating tumor DNA (ctDNA) mutation-based approach shows limited performance in minimal residual disease (MRD) detection, especially for landmark MRD detection at an early-stage cancer after surgery. Here, A total of 87 NSCLC patients, who received curative surgical resections (23 patients relapsed during follow-up), enrolled in this study. A total of 163 plasma samples, collected at 7 days and 6 months postsurgical, were used for high-throughput sequencing.

  Dataset EGAD00001010300

• BLUEPRINT release August 2016, Bisulfite-Seq for central memory CD8-positive, alpha-beta T cell, on genome GRCh38

  Bisulfite-Seq data for 2 central memory CD8-positive, alpha-beta T cell sample(s). 36 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002486

• BLUEPRINT release August 2016, RNA-Seq for monocyte, on genome GRCh38

  RNA-Seq data for 2 monocyte sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002375

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2392, on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2392 sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002359