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• RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial.

  DAC for RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial.

  Dac EGAC50000000627

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways

  A comprehensive constellation of somatic non-silent mutations and copy number (CN) variations in ocular adnexa marginal zone lymphoma (OAMZL) is unknown. By utilizing whole-exome sequencing in 69 tumors we define the genetic landscape of OAMZL. Mutations and CN changes in CABIN1 (30%), RHOA (26%), TBL1XR1 (22%), and CREBBP (17%) and inactivation of TNFAIP3 (26%) were among the most common aberrations. Candidate cancer driver genes cluster in the B-cell receptor (BCR), NFkB, NOTCH and NFAT signaling pathways. One of the most commonly altered genes is CABIN1, a calcineurin inhibitor acting as a negative regulator of the NFAT and MEF2B transcriptional activity. CABIN1 deletions enhance BCR-stimulated NFAT and MEF2B transcriptional activity, while CABIN1 mutations enhance only MEF2B transcriptional activity by impairing binding of mSin3a to CABIN1. Our data provide an unbiased identification of genetically altered genes that may play a role in the molecular pathogenesis of OAMZL and serve as therapeutic targets.

  Study EGAS00001006631

• Virginia PrIMeD Study

  The goal of this study was to determine whether screening children (2-16 yrs) in pediatric waiting rooms for genetic risk of type 1 diabetes (T1D) could be applied to diverse (by geography, genetic ancestry) communities, and for those at "high genetic risk," if barriers prevent subsequent screening for presence of islet autoantibodies. A total of 3,818 children were recruited from eight general pediatric and specialty clinics across Virginia. Clinical Research Coordinators were stationed at each clinic and obtained informed consent/assent, a brief medical history, and a saliva sample for DNA extraction and determination of their genetic risk using a T1D Genetic Risk Score (T1D GRS). Children were present in the clinic for a "healthy" visit, although children with and without a history of T1D were recruited into the study. Age, sex, self-reported ancestry/race, T1D history, and other medical history information was obtained. DNA was extracted from the saliva samples and genotyping with a T1D-focused array using 74 SNPs (including 26 SNPs in the HLA region) provided data to generate a T1D GRS for each individual. Of the 3,818 children recruited, there was a slight excess of males (1,959, 51.3%), a majority of white and Hispanic/Latino ancestry (82.8%), and 91 (2.4%) with prevalent T1D. A total of 542 (14.2%) had "high T1D genetic risk" (T1D GRS > 5). Although the T1D GRS included non-HLA genetic variants, 80% of those with "high genetic risk" would have been classified using only those SNPs in the HLA region alone. Of children with "high genetic risk" and without pre-existing T1D (n=494), 7.0% (34/494) consented for islet autoantibody screening. Among children with pre-existing T1D (n=91), 52% (n=48) also had a "high genetic risk." The HLA-focused T1D GRS was not significantly associated with age at onset of T1D. Of those at high genetic risk that consented for autoantibody testing (n=34) and completed the blood collection (n=28), two (2/28, 7.1%) tested positive for multiple autoantibodies and were at significant risk of developing T1D. Follow up of 55% of parents/guardians identified 2 (of 2,096, 0.095%) participants who developed T1D, one at "high genetic risk" and one with a first-degree relative with T1D. A major factor in obtaining islet autoantibody testing was concern over SARS-Cov-2 exposure and an independent non-scheduled blood collection.Individual-level data at each SNP (genotyped and imputed) for T1D genetic risk and affiliated data are provided in dbGaP.

  Study phs003609

• Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

  Gene expression profiles of single cells from 26 chemo-naïve and IDS tumor tissue and ascites samples from 17 HGSC patients

  Study EGAS50000000607

• dataset1

  Contains 14 control samples and 26 case samples.

  Dataset EGAD00001008576

• BLUEPRINT release August 2015, ChIP-Seq for CD8-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 5 CD8-positive, alpha-beta T cell sample(s). 26 run(s), 26 experiment(s), 26 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001513

• Women's Interagency HIV Study (WIHS)

  The Women's Interagency HIV Study (WIHS), a multicenter, prospective study, was established in August 1993 to carry out comprehensive investigations of the impact of HIV infection and its clinical, laboratory, and psychosocial effects in women. The purpose of this study is to collect and evaluate these data from HIV infected and at-risk women to better understand and provide support for women whom are currently HIV infected or who are at risk for HIV infection. Participants will have study visits every 6 months. Questionnaires regarding sexual behavior, health care utilization, medical and obstetric/gynecological history, psychosocial factors, and sociodemographics will be completed by participants. Physical, gynecological, and lipodystrophy examinations will also be conducted at each visit, and current medication regimen will be noted. Blood and other bodily fluid samples will be collected and registered in both local and national repositories of the WIHS in conjunction with NIAID.

  Study phs001503

• The NCAA-DoD Concussion Assessment, Research, and Education (CARE) Consortium

  Study Description: Established in 2014, the U.S. Department of Defense (DoD) and the National Collegiate Athletic Association (NCAA) funded the Concussion Assessment, Research and Education (CARE) Consortium to inform science, clinical care and public policy related to concussion and repetitive head impact exposure (HIE) in U.S. Military Service Academy (MSA) cadets and collegiate student-athletes. The primary aims of the initial study were to: (1) establish a multisite research consortium to characterize the effects of concussion and repetitive head impact exposure on brain health, (2) characterize the clinical sequelae and natural history of concussion, (3) characterize the effect of concussion and repetitive head impacts on brain structure and brain function. The 30 member institutions of the CARE Consortium (26 civilian universities/colleges and 4 military service academies) agreed to invite all varsity athletes to undergo multimodal clinical assessments at preseason baseline, and at 5 additional timepoints after concussion diagnosis. At the service academies, non-varsity athlete cadets/midshipmen were also studied. Assessment Categories At Each Time Point Baseline: • Demographics • Personal and Family History • Neurocognitive Assessment • Neurological Status • Postural Stability • Symptoms ACUTE POST-INJURY FOLLOW-UP (CARE 1.0) (24 hrs; 48hrs; Asymptomatic; Unrestricted Return to Play (RTP); 6 mos) • Neurocognitive Assessment • Neurological Status • Postural Stability • Symptoms CUMULATIVE & PERSISTENT EFFECTS. (CARE 2.0) In-Person Exit Visit; Post-grad Online • Demographics • Personal and Family History • Neurocognitive Assessment • Neurological Status • Postural Stability • Symptoms • PROs • MROs (at academies only) LONG-TERM EFFECTS (CARE/SALTOS Integrated (CSI))Annual Online Assessment (at MSAs only); In-Person Research Visits • Demographics • Symptoms • Psychological health • PROs • MROs (at academies only)A subset of athletes at 6 of the CARE institutions underwent additional assessments including multimodal MRI, proteomic and genomic biomarker characterization, and head impact quantification (helmet-based sensors). Assessment time points for the ARC/pARC Neurocognitive and Behavioral Testing was done at Baseline, <48hrs Post-Injury, Cleared for Return to Play Progression (Asymptomatic), Unrestricted Return to Play, 7 days following Return to Play, and at >60 days after final game of junior year until end of collegiate career.Blood biomarker collection was done at Baseline, <48hrs Post-Injury, Cleared for Return to Play Progression (Asymptomatic), 7 days following Return to Play, and at >60 days after final game of junior year until end of collegiate career. Multi-modal MRI studies were done at Baseline, <48hrs Post-Injury, Cleared for Return to Play Progression (Asymptomatic), 7 days following Return to Play, and at >60 days after final game of junior year until end of collegiate career. However, please note that only athletes from one study performance site completed a multi-modal MRI study at baseline.

  Study phs002175

• Dedifferentiated Melanoma (2021-02-02)

  De- and transdifferentiation of melanoma is a rare histopathological phenomenon that has not be characterised genetically. In this project we plan to sequence the genomes of de and transdifferentiated cases so as to define their genetic make-up. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006931