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• Sequence Data for DEEP Release August 2016

  DEEP (German Epigenome Project) sequence data of following samples (Sequencing Types: Chip-Seq, WGBS-Seq, RNA-Seq, sncRNA-Seq, NOMe-Se, DNase-Seq): 41_Hf01_LiHe_Ct, 41_Hf02_LiHe_Ct, 41_Hf03_LiHe_Ct, 01_HepG2_LiHG_Ct1, 01_HepG2_LiHG_Ct2, 01_HepaRG_LiHR_D31, 01_HepaRG_LiHR_D32, 01_HepaRG_LiHR_D33, 43_Hm01_BlMo_Ct, 43_Hm03_BlMo_Ct, 43_Hm05_BlMo_Ct, 43_Hm03_BlMa_Ct, 43_Hm05_BlMa_Ct, 43_Hm03_BlMa_TO, 43_Hm05_BlMa_TO, 43_Hm03_BlMa_TE, 43_Hm05_BlMa_TE, 51_Hf01_BlCM_Ct, 51_Hf03_BlCM_Ct, 51_Hf04_BlCM_Ct, 51_Hf02_BlCM_Ct, 51_Hf05_BlCM_Ct, 51_Hf06_BlCM_Ct, 51_Hf06_BlCM_T1, 51_Hf06_BlCM_T2, 51_Hf03_BlEM_Ct, 51_Hf04_BlEM_Ct, 51_Hf02_BlEM_Ct, 51_Hf05_BlEM_Ct, 51_Hf06_BlEM_Ct, 51_Hf06_BlEM_T1, 51_Hf06_BlEM_T2, 51_Hf03_BlTN_Ct, 51_Hf04_BlTN_Ct, 51_Hf02_BlTN_Ct, 51_Hf05_BlTN_Ct, 51_Hf06_BlTN_Ct, 51_Hf06_BlTN_T1, 51_Hf06_BlTN_T2, 51_Hf07_BmTM4_Ct, 51_Hf08_BlTM4_Ct, 51_Hf08_BmTM4_SP1, 51_Hf08_BmTM4_SP2, 51_Hf05_BlTA_Ct, 44_Mm01_WEAd_C2, 44_Mm03_WEAd_C2, 44_Mm02_WEAd_C2, 44_Mm07_WEAd_C2, 44_Mm04_WEAd_C1, 44_Mm05_WEAd_C1

  Dataset EGAD00001002527

• Sequencing data for oesophageal and related samples - Mourikis et al (WGS)

  Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. WGS (BAM files) 521 samples

  Dataset EGAD00001004775

• Deep exome sequencing

  Bam files from deep exome sequencing of blood DNA samples from five TET2 mutation carriers (Ly1, Ly2, Ly9, Ly11, Ly14) and three wild-type family members (Ly8, Ly10, Ly13) extracted at multiple time points. Library preparations were performed with SeqCap EZ Exome v3 (Roche, Switzerland) using six different index primers per sample for which paired-end Illumina sequencing was done with 75bp read length and HiSeq4000 sequencer. After alignment (bwa version 0.7.12), base recalibration (GATK 3.5), realignment around indels (GATK 3.5) and duplicate removal (MarkDuplicates; Picard Tools version 1.79), data from libraries with six different indexes were merged.

  Dataset EGAD00001004780

• miRNA-seq data for Molecular Characterization of ETMR

  This dataset contains miRNA-seq data from 10 patients. Small RNAs were isolated as described previously57,58 from fresh-frozen tumour material. In brief, total RNA was extracted using guanidinium isothiocyanate/phenol extraction followed by 3′-adaptor ligation of barcoded adenylated adaptors. Samples were pooled in two sets of five samples. Subsequently, gel electrophoresis was used to isolate small RNAs (19–35 nt) and purified using ethanol precipitation. Fragments were then amplified using standard PCR, isolated using gel electropho- resis and purified using ethanol precipitation. Samples were sequenced on a HiSeq 2000 v.4 machine resulting in 10 Fastq files.

  Dataset EGAD00001006218

• RNA of peripheral blood for pancreatic cancer and chronic pancreatitis

  Samples of nucleated cells found in peripheral blood from over 300 patients suffering from resectable pancreatic ductal adenocarcinoma, non-resectable pancreatic cancer, chronic pancreatitis, or none of these. Please cite this article when using data: Al-Fatlawi, A.; Malekian, N.; García, S.; Henschel, A.; Kim, I.; Dahl, A.; Jahnke, B.; Bailey, P.; Bolz, S.N.; Poetsch, A.R.; Mahler, S.; Grützmann, R.; Pilarsky, C.; Schroeder, M. Deep Learning Improves Pancreatic Cancer Diagnosis Using RNA-Based Variants. Cancers 2021, 13, 2654. https://doi.org/10.3390/cancers13112654

  Dataset EGAD00001006915

• Circulating cell-free DNA analyses for Patient Monitoring in Small Cell Lung Cancer

  This study consists of over 200 data files from cfDNA and germline DNA from 69 patients and 32 healthy normal volunteers discussed in this publication.

  Dataset EGAD00001007070

• Vumc_organoids

  Organoid cultures derived from normal colon and/or colorectal adenomas and/or colorectal carcinomas. RNA and DNA was isolated from these cultures for genome wide profiling.

  Dataset EGAD00001008479

• Sequence data for study: Mobilization of tissue-resident memory CD4+ T lymphocytes from bone marrow and their contribution to a systemic secondary immune reaction

  Short Description: This study contains 7 RRBS samples, including 3 ex vivo CD4+ Trm (2 x spleen and 1 x bone marrow) and 4 blood tetanus (TT) and measles (Me) antigen-reactive memory CD4+ cells before and one day post DTaP (diphtheria-tetanus-pertussis) and MMR (measles-mumps-rubella) vaccination, respectively (1 x tetanus D0, 1 x tetanus D1, 1 x measles D0, 1 x measles D1). Technology: Illumina HiSeq 2500 Filetype: fastq format

  Dataset EGAD00001007886

• WGS data for ATLAS paper (123 patients)

  WGS data of multi-region samples from PLANET 123 Patient cohort

  Dataset EGAD00001009858

• Sequencing data for oesophageal and related samples - Zamani et al

  Data supporting: "Genomic and epidemiological similarities between phenotypically distinct esophageal adenocarcinoma suggest a single entity" Zamani et al

  Dataset EGAD00001015435