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• Normal sample for patient SA666

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA666

  Dataset EGAD00001009604

• Tumour sample for patient SA1065

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1065

  Dataset EGAD00001009605

• Tumour sample for patient SA1064

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1064

  Dataset EGAD00001009606

• Tumour sample for patient SA1026

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1026

  Dataset EGAD00001009607

• Tumour sample for patient SA1069

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1069

  Dataset EGAD00001009608

• Tumour sample for patient SA1017

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1017

  Dataset EGAD00001009609

• Tumour sample for patient SA1027

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1027

  Dataset EGAD00001009610

• Tumour sample for patient SA1073

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1073

  Dataset EGAD00001009611

• Tumour sample for patient SA1074

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1074

  Dataset EGAD00001009612

• Tumour sample for patient SA576

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA576

  Dataset EGAD00001009613

• Tumour sample for patient SA1028

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1028

  Dataset EGAD00001009614

• Tumour sample for patient SA1040

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1040

  Dataset EGAD00001009615

• Tumour sample for patient SA992

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA992

  Dataset EGAD00001009616

• Tumour sample for patient SA610

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA610

  Dataset EGAD00001009617

• Normal sample for patient SA416

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA416

  Dataset EGAD00001009618

• Normal sample for patient SA1070

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1070

  Dataset EGAD00001009619

• Tumour sample for patient SA1070

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1070

  Dataset EGAD00001009620

• Tumour sample for patient SA997

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA997

  Dataset EGAD00001009621

• A73044B

  Whole genome sequencing for single cells for library A73044B 2085 cells; filetype=bam

  Dataset EGAD00001007101

• A73047D

  Whole genome sequencing for single cells for library A73047D 2091 cells; filetype=bam

  Dataset EGAD00001007102

• A95633B

  Whole genome sequencing for single cells for library A95633B 2259 cells; filetype=bam

  Dataset EGAD00001007104

• A96115A

  Whole genome sequencing for single cells for library A96115A 1635 cells; filetype=bam

  Dataset EGAD00001007111

• A96193B

  Whole genome sequencing for single cells for library A96193B 2410 cells; filetype=bam

  Dataset EGAD00001007118

• A96240B

  Whole genome sequencing for single cells for library A96240B 1683 cells; filetype=bam

  Dataset EGAD00001007122

• Analysis of Treg gene expression patterns by RNA-Seq in patients with rheumatoid arthritis (RA) and healthy controls (HCs) : Comparison between young and elderly individuals

  We compared the gene expression of CD4+CD45RA-CD25hiCD127lo Treg cells from PBMCs between young and elderly RA patients and HCs by RNA-seq

  Study JGAS000693

• Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma

  We analyzed the genome of plasma cells collected from bone marrow samples or plasmocytoma from patients prior to (when available) and progression on anti-GPRC5D T cell engagers.

  Study EGAS50000001148

• Age-dependent association of clonal hematopoiesis with COVID-19 mortality in patients over 60 years

  Genomic DNA extracted from peripheral blood of COVID-19 patients (n = 241 deceased, n = 239 survivors) was sequenced with the Myeloid Solutions™ panel of SOPHiA Genetics.

  Study EGAS50000000001

• Indigenous American Genomic Diversity Project (IAGDP).

  Here we present the Indigenous American Genomic Diversity Project (IAGDP), comprising 128 newly generated high-coverage (NGS; ~44X) whole genomes from Indigenous individuals across eight Latin American countries, representing 45 populations and 28 language families. This dataset expands Indigenous representation in genomics, with emphasis on geographically and linguistically diverse populations, particularly from the South American lowlands.

  Dataset EGAD50000002396

• Dynamic human admixture histories over the past ~1,300 years at the northern Himalayan frontier

  Whole-genome sequencing data from ten present-day individuals from Himachal Pradesh, India. DNA from these ten present-day individuals was converted to double-stranded libraries and sequenced on Illumina NovaSeq 6000 in 150 bp paired-end mode. The dataset consists of raw fastq and bam (hg19) files.

  Dataset EGAD50000001925

• WGS of Newly Diagnosed and Refractory/Relapsed Multiple Myeloma

  This dataset includes paired tumor and non-tumor WGS data from patients diagnosed with newly diagnosed (n = 6), refractory/relapsed multiple myeloma (n = 3) or plasma cell leukemia (n = 1). These samples presented >95% tumor PCs in bone marrow aspirates. Plasma cells and T cells (non-tumor cells) were isolated from bone marrow aspirates using a magnetic approach.

  Dataset EGAD50000001177

• MS meninges single nuclei RNA sequencing

  10X 3' (RNA) samples of isolated single nuclei from highly inflamed leptomeninges and adjacent grey matter from 3 MS patients used in the paper.

  Dataset EGAD50000001235

• A thymic ILC1-like progenitor with differentiation potential towards KIR+NKG2A- NK cells

  The dataset contains bulk RNA sequencing data from 12 pediatric thymus samples collected during cardiac surgeries. These samples represent immunologically healthy donors with a mean age of 6 months. The sequencing was performed using Illumina HiSeq4000, and the processed files are available in standard formats such as FASTQ.

  Dataset EGAD50000001120

• Hi-C in breast healthy, primary cancer and metastatic tissues

  Hi-C libraries have been prepared by enzymatic digestion with MboI restriction enzyme and sonication (Covaris). Illumina single-indexig primers have been use to amplify ligated fragments. Hi-C experiments have been performed on 10 slices (50um thick) of fresh-frozen tissues or 10x10e6 Pleural Effusion cells. Raw paired-end fastq.gz files are provided.

  Dataset EGAD50000000643

• GIST Whole Genome Sequencing

  Whole genome sequencing of tumour and normal samples from familial GIST. Multiple family members were affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene, (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877C>T; p.Arg293*, pR293X).

  Dataset EGAD50000000549

• Total RNA sequencing of fibroblasts from an control individual

  Total RNA sequencing of fibroblasts from an individual with 30-55x GCC repeats in the FMR1 5'UTR. Libraries were prepared with total RNA with Ribo-Zero ribosomal RNA depletion (illumina), and sequenced paired-end, 75bp on a NextSeq 550 system. This dataset contains three RNA-sequencing replicates from the same cell line.

  Dataset EGAD50000000922

• RNAseq Data Cyr61-MAC and HUVEC

  Gene expression of MAC enriched by adhesion to Cyr61 in comparison to HUVEC. This dataset includes RNAseq Data from myeloid angiogenic cells (MAC) enriched from peripheral blood by adhesion to Cyr61 (4 samples prepared from different donors) and of human umbilical vein endothelial cells (HUVEC) (4 samples). Illumina NextSeq500 technology was used. FASTQ data are provided.

  Dataset EGAD50000000758

• Fecal metagenomics and plasma metabolomics

  This dataset contains all fecal shotgun metagenomics and metabolomics of the study which investigated the effects of the probiotic strain Anaerobutyricum soehngenii. Shotgun data is from three different time points, baseline and two follow up. Metabolomics sets are pre and post intervention, both fasted and post prandially. Data on randomization and metformin use can be found in the analysis.

  Dataset EGAD50000000608

• Fragmentomics profiling and quantification of plasma Epstein-Barr virus DNA enhance prediction of future nasopharyngeal carcinoma.

  This dataset included human plasma EBV DNA target-capture sequencing data. The capture probes were designed to cover the entire EBV genome and selected human autosomal regions. After enrichment, the products were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19) in BAM format.

  Dataset EGAD50000000580

• T-ALL RNA-Seq raw data files

  The data set consists of unprocessed RNA-Seq data from 225 patients diagnosed with T cell acute lymphoblastic leukemia in fastq file format. Samples from bone marrow or peripheral blood were subjected to mRNA library prep using Poly-A selection and sequencing on a NovaSeq 6000 system yielding approximately 30 million reads per sample.

  Dataset EGAD50000000308

• Single-cell RNA-sequencing of peripheral blood mononuclear cells from patients with achalasia

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peripheral blood mononuclear cells (PBMC) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000250

• Results of RNA sequencing from all patients/samples

  Results of sequencing the targeted RNA-seq panel of breast cancer patients and controls. This dataset comprises of FASTQ files of 295 samples (both breast cancer patients and controls) and the results of mapping the FASTQ files to the reference human genome (hg38) available in a form of raw gene expression matrix.

  Dataset EGAD50000000017

• methylation_bc_cervix

  Raw methylation data from cervical samples in individuals with breast cancer.

  Dataset EGAD00010002081

• methylation_ctrl_cervix

  Raw methylation data from cervical samples in controls.

  Dataset EGAD00010002079

• EGAD00000000045

  Genomic sequencing and transcriptome shotgun sequencing of a metastatic tumour and its recurrence after drug therapy in a single patient

  Dataset EGAD00000000045

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 4)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one ETV6::RUNX1 ALL patient (ALLK-132). Novogene's internal method was used in directional library preparation including rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002590

• Oral Microbiome HPP cohort raw sequencing data

  Raw metagenomic sequencing data from oral swab samples collected as part of the Human Phenotype Project (HPP) longitudinal cohort study at the Weizmann Institute of Science. The dataset comprises 7,948 single-end FASTQ files generated using Gencove low-pass whole genome sequencing. Samples represent the oral microbiome of healthy adult participants. Data access is restricted in accordance with participant informed consent.

  Dataset EGAD50000002532

• The natural history of clonal haematopoiesis: phase 6 targeted

  Deep targeted sequencing of 56 genes associated with clonal haematopoiesis and haematological malignancy in peripheral blood-derived DNA from 11 older adults, each previously sampled 2-5 times over the preceding ~13 years.

  Dataset EGAD00001007683

• Single-cell RNA-seq of AML blasts pre and post culture

  This dataset contains 6 Fastq files from 3 samples (pre-culture (n=1), post culture in standard (n=1) or niche-llike (n=1) conditions) from 1 AML patient. They correspond to single-cell RNA sequencing on Illumina plateform of 3 libraries prepared with 10X Genomics gene expression V3.1 chemistry.

  Dataset EGAD00001008772

• Understanding the multicellular dynamics of clear cell renal cell carcinoma - spatial transcriptomics

  The dataset comprises of transcriptomes of tissue sections derived from either the tumour normal interface or tumour core from clear cell renal cell carcinomas. 16 sections are sampled in total using 10x Genomics' Visium technology.

  Dataset EGAD00001008781

• FFPE CRC sequence data and somatic variants

  We included 3 BAM files of the genome sequencing data: 2 of 3 are from tumour samples, namely 1 repaired-FFPE and 1 unrepaired FFPE; the third BAM file is from normal tissue of FFPE block. There is also a VCF file containing all somatic mutations in the dataset.

  Dataset EGAD00001007723