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• scRNA seq and scTCR seq data from 5 melanoma patients

  The Chromium Controller and Chromium X platfor of 10X Genomics were used for single cell partitioning and barcoding. Each cell's transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 5' Gene Expression (GEX), V(D)J and Feature Barcode (FB) Libraries were prepared according to the manufacturer's protocols (CG000330 and CG000331, 10X Genomics). All libraries were quantified and normalized on library QC data generated on the Bioanalyzer system according to manufacturer's protocols (G2938-90321 and G2938-90024, Agilent Technologies). Based on the expected target cell counts, a balanced library sub-pool of samples was compsed for SC5'GEX, V(D)J and FB libraries. Library sub-pools were quantified by qPCR, accodring to the KAPA Library Quantification Kit Illumina(R) Platforms protocol (KR0405, KAPA Biosystems). Based on qPCR results a final sequencing pool was composed. Paired end sequencing was performed on a NovaSeq 6000 Instrument (Illumina) using NovaSeq 6000 Reagent Kits v1.5 100 cycles (cat. no. 20028401, 20028319, 20028316 Illumina), using 28 cycles for Read 1, 10 cycles for Read i7, 10 cycles for Read i5 and 90 cycles for Read 2.

  Dataset EGAD50000001155

• Novel Epigenetic Markers for Toxicity after Intraoperative and Conventional Radiotherapy for Breast Cancer

  Ionizing radiation is a common treatment option for cancer but its use is limited by the unpredictable and highly heterogeneous onset of late side effects, especially radiation-induced fibrosis. Clinically applicable biomarkers and effective treatments for radiation fibrosis are currently unavailable. In order to identify novel markers we ran a genome-wide DNA methylation screen in primary dermal fibroblasts obtained from breast cancer patients before intraoperative radiotherapy. Cells from patients developing fibrosis within a three-year follow up were compared to those without fibrosis (12 individuals per group). Illumina Infinium HumanMethylation450 BeadChip Technology was used.

  Study EGAS00001001279

• The_Causes_of_Clonal_Blood_Cell_Disorders_Study___SCOR

  We will take a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We will grow these up into colonies, then whole genome sequence each colony. Somatic mutations will act as a unique barcode for each clone. We will then design a panel for targeted resequencing of the mutations that we find. It will then be possible to look for these mutations in the peripheral blood over several years, to see the dynamics of how HSCs contribute to the peripheral blood in health.

  Study EGAS00001002132

• Non-invasive prenatal diagnosis by genome-wide haplotyping of maternal cell-free plasma DNA

  Whereas non-invasive prenatal testing for aneuploidies (NIPT-A) is widely implemented, non-invasive prenatal testing for monogenic diseases (NIPT-M) is lagging. By capturing and targeted sequencing of 250000 polymorphic SNP loci from maternal plasma circulating cell-free DNA (cfDNA) and DNA from relatives, the fetal haplotype and chromosomal copy numbers are deduced. In all families tested, the cfDNA derived haplotypes are on average 97% concordant with the neonatal and embryo haplotype. This generic non-invasive prenatal diagnostic approach allows cost efficient scrutinizing the fetal genome for the presence of any inherited monogenic disease or trait.

  Study EGAS00001003634

• Treatment of Pulmonary Hypertension and Sickle Cell Disease with Sildenafil Therapy (Walk-PHaSST)

  Pulmonary arterial hypertension (PAH) is a progressive condition characterized by narrowing or stiffening pulmonary arterioles resulting in increased pulmonary blood pressure and reduced delivery of oxygenated blood to the body. It is a common complication of sickle cell disease and initially presents with the symptom of shortness of breath (dyspnea) on exertion. As the condition worsens, other symptoms such as dizziness, lower extremity edema, and chest pain can develop. The drug, sildenafil, works by relaxing blood vessels in the lungs which reduces pulmonary blood pressure and allows more oxygenated blood to circulate. Increased levels of oxygenated blood allows individuals with PAH to tolerate more activity, but guidelines for using sildenafil in patients with PAH and sickle cell disease were unavailable at the time of the Walk-PHaSST trial.Participants were screened for the existence of pulmonary hypertension with a six minute walk test and a Doppler echocardiogram that assessed TRV, diastolic function, and valvular and systolic function. Subjects with TRV ≥ 2.7 m/s received further clinical evaluation for possible causes of pulmonary hypertension. Other screening data included medical history, a physical exam, and standard laboratory testing. For individuals with moderate to severe pulmonary hypertension (TRV ≥ 3.0), a cardiac catheterization was done at the baseline and week 16 data collection periods.Subjects eligible for the main intervention trial based on screening results were randomized in a 1:1 double blind fashion to receive sildenafil or placebo for 16 weeks. Subjects received 20 mg of oral sildenafil or matching placebo 3 times daily for 6 weeks, followed by 40 mg 3 times daily for 4 weeks, followed by 80 mg 3 times daily for 6 weeks, as tolerated. Participants could also receive other therapies as needed to manage sickle cell and related complications. The primary outcome measure of the trial was change in the six minute walk test, a standard indicator of a person's heart and lung function and exercise capacity, from baseline to week 16. After completing the study treatment (or placebo), participants could choose to be part of the open-label follow-up phase of the study and continue to be assessed for up to one year.The study was intended to screen about 1000 subjects and randomize 132 subjects, however it was terminated early due to the unforeseen increase in adverse events in participants treated with sildenafil as compared to placebo. When the study was stopped, 33 participants had completed the trial. Subjects continued to be monitored, but were instructed to taper sildenafil treatment over three to seven days.There was no evidence that treatment with sildenafil impacted the six minute walk distance from baseline to week 16. In addition, treatment with sildenafil appeared to increase rates of hospitalization due to sickle cell disease pain.Due to in part to the early termination of the trial, the majority of subject data was collected from the screening phase of the study (n=720), as opposed to the main intervention trial (n=74).Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

  Study phs002383

• sc-DECISION

  Data derived from PBMC and blood samples for the single cell and bulk RNAseq analysis for the sc-DECISION paper. https://doi.org/10.1101/2025.02.04.25321370

  Dac EGAC50000000642

• Preeclampsia InterPregGen Consortium: GWAS meta-analysis summary statistics for European fetal preeclampsia cases versus controls and GWAS genotype data for European fetal preeclampsia cases

  Study EGAS00001001048

• Dataset for TIX

  All files for TIX individuals

  Dataset EGAD50000000426

• RNAseq for 4 pdx and 1 cell-line

  RNAseq for #1049, #111, #1217, #206, COV362

  Dataset EGAD50000000032

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000853