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• WGS of low-count and high-count MBL

  The cohort consisted of individuals with low-count MBL, high-count MBL as well as patients with CLL. Whole genome sequencing was initially performed in a smaller cohort of selected, representative samples, while targeted re-sequencing of CLL putative driver genes was performed in all samples of the cohort. Besides CLL cell samples, the sequencing process was performed in paired control samples including both buccal and polymorphonuclear cell samples.

  Dataset EGAD50000000629

• Bulk RNAseq of cultured fibroblasts

  Fastq files from bulk RNAseq of fibroblasts after culture and facs sorting (N=9). Sorted FAP+ CAF cells RNAs were extracted using Qiagen miRNeasy Kit (Qiagen, #217004) according to the manufacturer's instructions. Verification of RNA integrity and quality was performed using the Agilent RNA 6000 nano Kit (Agilent Technologies, #5067-1511). cDNA libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina, #20020594) followed by sequencing on NovaSeq (Illumina).

  Dataset EGAD50000000323

• RNA-seq dataset of A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study describing the differentiation trajectory of atypical teratoid rhabdoid tumors (ATRTs) at single-cell level. This study describes how the differentiation trajectory differs per subtype of ATRTs, and how those findings could contribute to develop so-called "maturation therapy" tailored towards ATRTs.

  Dataset EGAD00001015544

• Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors

  Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors. The sequencing was done on HiSeq 4000 with the SmarTer Ultra Low Input RNA v4 and NEBNext ChIP-Seq Kit. The TAMs were treated with GW2580, BLZ945 and PLX3397 and DMSO as control.

  Dataset EGAD00001011273

• The BNT162b2 mRNA COVID-19 vaccine induces long-term effects on both adaptive and innate immune responses

  This dataset contains bulk RNA sequencing at different timepoints post-BNT162b2 mRNA COVID-19 vaccination. Stimulation experiments were performed at each of the timepoints (RPMI, Influenza, R848 and Influenza stimuli), resulting in 242 libraries distributed over 4 stimulations and 4 timepoints. Libraries were sequenced on the DBNSEQ platform.

  Dataset EGAD00001011042

• low pass WGS of patient from the CN300 cohort

  We copy number profiled 688 tumor regions from 300 patients presenting with advanced prostate cancer and prospectively followed-up (median, 7 years) in the control group of the STAMPEDE trial. Patients were categorised into four metastatic states, namely high-risk non-metastatic (with or without local lymph node involvement) or metastatic (low or high volume).

  Dataset EGAD00001008800

• RNA-Seq of response to Tozinameran vaccination in individuals with KTx/dialysis or healthy controls.

  Low-input RNA-Seq (~200 cells per sample) of CD4+ T cells in patients with kidney transplants, dialysis, or healthy controls after the second dose of Tozinameran COVID-19 vaccine. RNA-Seq was performed using the Smart-Seq v4 ultra-low input protocol. The dataset includes 4 healthy control samples, 3 kidney transplant recipients, and 4 patients undergoing dialysis.

  Dataset EGAD00001007689

• MiRNome_pituitary_adenoma

  Small RNA (<100 bases in length) were purified from total RNA using miRNeasy kit (Qiagen), then sequenced. Libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq small RNA protocol (Illumina), starting from 1 µg of high quality total RNA. Single read (1 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on miRBase v.2052, then counted with STAR (v.2.5.2a).

  Dataset EGAD00001004998

• Methylation profiling by MCC-Seq of visceral fat (N=199) and whole-blood (N=206) derived from IUCPQ participants

  The study includes NGS-based methylC-capture sequencing (MCC-Seq) on 199 visceral adipose tissue and 206 whole-blood DNA samples derived from obese individuals (BMI >40 kg m-2) in the IUCPQ cohort. We generated 100bp paired-end reads using the Illumina HiSeq2000 or 2500 systems.

  Dataset EGAD00001004787

• Bajau and Saluan adaptation study data

  This dataset includes whole genome sequencing data from 93 Bajau and Saluan individuals that were used in the Ilardo et al 2018 study on adaptation to diving in Sea Nomads. Sequencing libraries were built using the TruSeq Nano DNA Library Preparation Kit on an Illumina NeoPrep instrument. Each pool was sequenced 125 Paired-End over one or two lanes on the Illumina HiSeq2500 (version 4 chemistry). Samples were sequenced to an average depth of 5x.

  Dataset EGAD00001004207

• A case of colorectal cancer with ERBB2 c.2264T>C (p.Leu755Ser) mutation

  This data set contains next generation sequencing (NGS) data of two serial tumor samples (primary and a metastasis) from a patient with colorectal cancer showing an ERBB2 c.2264T>C (p.Leu755Ser). NGS was performed using the Illumina TruSeq Amplicon Cancer Panel (TSACP, Illumina) covering 212 amplicons in 48 cancer associated genes on the Illumina MiSeq sequencing platform. The dataset contains two BAM files.

  Dataset EGAD00001002252

• Leiden_melanomafamilies

  Around 10% of patients who present in melanoma clinics have a first degree relative with a previous diagnosis of melanoma. While around 3% have three or more relatives who have been diagnosed with the disease. In this project we will whole genome sequence patients from large Dutch familial melanoma pedigrees to identify mutations in genes that drive melanomagenesis. The identification of these genes will facilitate the management of familial melanoma patients and their families.

  Dataset EGAD00001002186

• Detecting PKD1 variants in Polycystic Kidney Disease patients by single-molecule long-read sequencing

  Cohort of 19 ADPKD patients characterized using long-read sequencing. The variant identification provided high sensitivity in identifying PKD1 pathogenic variants, with a diagnostic yield of 94.7%. This dataset includes all sequencing data (BAM files) of the 19 patients, in addition to their raw variants (unfiltered) obtained from the long-read sequencing as well as Sanger sequencing (VCF file).

  Dataset EGAD00001003103

• Reproducibility of variant calls in replicate next generation sequencing experiments

  To examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA, we performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. This data set contains 17 breast cancer samples that were sequenced in duplicate (n=14) or triplicate (n=3), in order to assess concordance of all calls and single nucleotide variant (SNV) calls.

  Dataset EGAD00001001209

• RNA sequencing data of pediatric BCR::ABL1 acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one BCR::ABL1 ALL patient (ALLT-399). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002580

• RNA sequencing data of pediatric KMT2A-rearranged acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one KMT2A-r ALL patient (ALLT-355). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002583

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 3)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one ETV6::RUNX1 ALL patient (ALLT-397). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002587

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one hyperdiploid ALL patient (ALLT-356). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002593

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 4)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of three hyperdiploid ALL patients (ALLT-382, ALLT-395, ALLK-111). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002596

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of three B-other ALL patients (ALLT-357, ALLT-361, ALLK-108). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002597

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 5)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one B-other ALL patient (ALLT-396). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002601

• Landscape of Intratumoral NK Cell and ILC in Head and Neck Squamous Cell Carcinoma

  In this study, total innate lymphoid cells (ILCs), including natural killer (NK) cells, were FACS-sorted from eight dissociated primary head and neck squamous cell carcinoma (HNSCC) tumors. In addition, ILCs and NK cells were sorted from peripheral blood of tumor patients. The ILCs and NK cells were analyzed by single-cell RNA sequencing (scRNA-seq) using the Smart-seq2 approach.

  Study phs002002

• Single Cell Omics Resolves Transcriptional Alterations in Sjogren's Syndrome

  Single cell omics resolves transcriptional alterations in Sjogren's Syndrome. This data compares the single cell transcriptional profiles of the minor salivary glands between Sjogren’s Syndrome patients and non-Sjogren’s Syndrome subjects. Portions of this data were reported in two separate publications: Huang & Perez, et al., 2021 Nature Medicine and Yin, et al., 2021, Frontiers in Immunology . 

  Study phs002446

• DDX50 Cooperates With STAU1 to Effect Stabilization of Pro-Differentiation RNAs

  This study was undertaken to determine the role of DDX50 in epidermal homeostasis. Primary neonatal foreskin keratinocytes were obtained from discarded surgical samples at a California hospital. Samples were anonymous and not selected. DDX50, which was associated with STAU1, was found to promote epidermal differentiation and transcript stability using the methods of RNA-seq, CLIP-seq and DMS-MaP-seq.

  Study phs003766

• HipSci HumanExome BeadChip analysis - Hereditary Cerebellar Ataxias

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Cerebellar Ataxias.

  Study EGAS00001002005