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• 10x Genomics BCR Sequencing

  BCR sequencing done with 10x Genomics V(D)J kit + platform for the paper: Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma. Dataset contains paired FASTQ files for 35 samples, each was processed with the 10x Genomics V(D)J kit to obtain the sequence of the B-cell receptor sequence.

  Dataset EGAD50000001373

• Smart-seq2 analysis of 11 ETMR patient samples (4,031 high-quality single cells/nuclei).

  We analyzed 11 ETMR patient samples using single-cell transcriptomics (6 from fresh and 5 from frozen material). Samples were profilied by paired-end scRNA-sequencing using the Smart-Seq2 protocol on a NextSeq 500 sequencer (Illumina). The dataset contains 8,062 fastq files of 4,031 high-quality single cells/nuclei. Raw fastq files of high-quality cells are shared.

  Dataset EGAD50000001379

• Tumor Profiler Project - OV bulk transcriptomics data additional samples

  The dataset contains bulk transcriptomics data from 4 samples from 3 different patients with ovarian cancer. 3 samples were collected from the tumor, 1 sample from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. These samples are from patients not classified as as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001411

• 10Xchromium 3' RNA-seq of 21 samples from human embryonic heart

  21 samples were taken from human embryonic heart of PCW 5.5-14 of a total of 13 fetuses. Samples were subject to 10Xgenomics chromium single cell 3' sequencing version 2 or 3. Data was analyzed using STARSolo version 2.7.10a, using human genome GRCh38.p12 and transcript annotations from ENSEMBL release 93 from reference package GRCh38-3.0.0 as available from 10Xgenomics.

  Dataset EGAD50000001499

• M116 DNA Methylation Array

  DNA samples were quantified with Qubit BR kit on a Qubit2.0 fluorimeter (ThermoFisher Scientific), and integrity was checked using agarose gel electrophoresis. DNA from samples passing the quality control was bisulfite-converted using the EZ DNA Methylation-Gold™ Kit (Zymo Research, Cat. D5005) following the manufacturer's instructions. Then, bisulfite-converted DNA was hybridized into the Methylation EPICv1.0 BeadChip (Illumina) array interrogating > 850,000 CpG sites according to manufacturer's instructions

  Dataset EGAD50000001678

• RNA sequencing of baseline HCC PDX models

  To establish the baseline transcriptional profiles, we performed bulk RNA-seq for 36 of our HCC PDX models. 2-6 samples were collected for each model resulting in a total of 68 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000736

• CASCADE tumour high-coverage whole genome sequencing data

  High coverage whole genome sequencing data (total: 22; median coverage: ~56X; range: 27X – 82X) from fresh frozen postmortem tissues harvested from patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.

  Dataset EGAD00001009491

• Raw sequencing data from low-input chromosome conformation capture in CD4+ T cells

  This dataset contains raw sequencing data from low-input PCHi-C in human primary CD4+ T cells isolated from healthy donors. The data are released as paired-end Illumina FASTQ files. Promoter Capture Hi-C used DpnII digestion and Tn5-based low-input library preparation, followed by targeted capture with custom-designed biotinylated RNA probes targeting most of the annotated gene promoters.

  Dataset EGAD50000001873

• scRNAseq of fresh CRC punch biopsies

  The dataset includes single-cell RNAseq data generated by Plate-Seq technology from scDiscoveries. The dataset contains samples from a total of 5 different early CRC biobank patients (pt5, pt11, pt13, pt14, pt16) from 4 different sequencing runs. Punch biopsies of different regions of the tumor (Core, Invasive front and, if available, Adenoma) were FACS sorted onto plates prior to sequencing.

  Dataset EGAD50000002203

• Metadata Submission

  Metadata Submission Welcome to the EGA Metadata Submission landing page. Here, we provide you with essential resources to facilitate a seamless submission process. Before starting your submission, please make sure you check the following pages: Submission FAQ Submission Quickguide Submission account terms EGA metadata schema If you want to submit sequencing and/or phenotypic data check these pages: Submitter Portal Submitter Portal API If you want to submit array data check these pages: Array documentation Webin Webin API

  Documentation submission/metadata/submission