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• Human Companion Data for 'A Transcriptomic Atlas of Mouse Cerebellar Cortex Reveals Novel Cell Types'

  In this study, we used single-nucleus RNA-seq to comprehensively define the cell specialization of the mouse cerebellar cortex and vermis. We focused in particular on two interneuron populations—the unipolar brush cells (UBCs) and the molecular layer interneurons (MLIs), identifying continuous variation within the former population, and a new discrete axis of variation in the latter. Human postmortem tissue was used to demonstrate that these specializations are evolutionarily conserved in primates. Together, these findings provide the first comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological, and physiological ontologies for defining brain cell types.

  Study phs002414

• Ultra-deep Error-corrected Sequencing of Peripheral Blood for Clonal Hematopoiesis in Patients Undergoing AAA Surgery

  Patients undergoing elective abdominal aortic aneurysm (AAA) surgery were enrolled to investigate the prevalence and characteristics of clonal hematopoiesis. Peripheral blood was collected at the time of surgical admission using PAXgene DNA tubes. Genomic DNA was extracted and subjected to ultra-deep error-corrected targeted sequencing using a custom gene panel covering recurrent clonal hematopoiesis-associated genes. Sequencing libraries were prepared following established protocols and sequenced on an Illumina NovaSeq X system. The resulting dataset includes paired-end FASTQ files for each participant, enabling high-sensitivity detection of somatic variants down to low variant allele frequencies. This study provides a comprehensive sequencing resource for evaluating clonal hematopoiesis in AAA patients.

  Study JGAS000864

• Sickle Cell Disease Natural History Data Resource (SCD NHDR)

  Data Access NOTE Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. BackgroundThe NHLBI initiated the Sickle Cell Disease Natural History Data Resource (SCD NHDR) to leverage existing SCD studies to build a data resource to provide phenotypic data on contemporaneous control cohorts for gene therapy trials and other studies. The potential uses of the NHDR are broad, including providing matched controls for clinical trials, observing a cohort of untreated patients as part of a natural history study, or conducting comparative effectiveness research on a subpopulation with selected co-morbidities or drug treatment profiles. The SCD NHDR includes two multi-center SCD longitudinal cohort studies with extensive annual clinical data and patient surveys, the Sickle Cell Disease Implementation Consortium (SCDIC-I and SCDIC-II) and the Globin Research Network for Data and Discovery (GRNDaD). The SCDIC-I, initiated in 2017 and concluded in June 2022, enrolled over 2400 patients with SCD from 8 US treatment centers. The SCDIC-II reconsented 1220 of the SCDIC-I patients as well as enrolling an additional 450 new patients from the same 8 centers between September 2022 and October 2023, for a total of 1670 in SCDIC-II. Only two of the many GRNDaD centers are submitting data to the SCD NHDR for deposit into BDC (approximately 122 patients). Data submissions from the SCD NHDR to BDC will be annually starting in early 2024. Description of the Study Data All data obtained for the SCD NHDR are considered common data elements (CDEs) important for studies of SCD. These CDEs were identified from several workgroups of SCD experts convened under the NHLBI's Cure-SC Initiative (https://curesickle.org/cde-catalog). The following types of data elements were abstracted from the medical record – variables that describe the SCD diagnosis, SCD co-morbidities and other clinical complications, elements from the physical examination, medications and transfusions, insurance type, laboratory measurements, healthcare utilization, history of SCD-related procedures, and measurements from cardiac procedures. The following types of data were self-reported on the patient survey – demographics, diagnosis information, pain experience, social and mental health information, other patient reported outcome domains (e.g., sleep, fatigue), and alcohol and smoking history. Standard PRO measures were used from ASCQ-Me, PROMIS and Neuro-QoL. Patient surveys were completed approximately annually. Under SCDIC-I, two medical record abstractions and labs were reported at enrollment and approximately 3 years later. Under SCDIC-II and GRNDaD, all data are collected annually. Patients may refuse to complete the survey.

  Study phs003529

• HCC cfMeDIP-seq

  This dataset comprises 406 raw fastq files derived from 203 plasma cfDNA samples from 90 patients diagnosed with hepatocellular carcinoma (HCC). The samples include 90 baseline HCC (b-HCC) samples, collected during liver transplant or resection surgeries, and 113 postoperative follow-up (f-HCC) samples. For each sample, 10ng of cfDNA was used for library preparation utilizing cfMeDIP-seq technology based on the 5mC antibody-immunoprecipitation strategy. Libraries were validated via Bioanalyzer trace analysis and sequenced on Illumina NovaSeq 6000 or HiSeq 2500 platform with paired-end 150-bp (NovaSeq) or 125-bp (HiSeq) model for ~100 million reads per sample.

  Dataset EGAD50000000651

• RNA sequencing of Notch inhibitor treated HCC PDX models across timepoints

  To study the effect of Notch inhibition on the transcriptional profiles our PDX models, we generated bulk RNA-seq data for two Notch inhibition sensitive and three Notch inhibition insensitive models across multiple timepoints (8h, 24h, 48h, 7d, 17d) using anti-JAG1, anti-Notch2, anti-Notch1 or anti-gD antibodies. 3-5 samples were collected for each treatment condition, resulting in a total of 96 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 EGAD50000000737

• 10X single-cell Multiome (RNA+ATAC) and single-cell RNAseq of xenograft-derived HSPC, progenitors and myeloid progeny

  10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries for human HSPC sorted from xenografts recovered from inflammatory challenge. 10X genomics 3' kits were used to prepare single-cell RNA-seq libraries for committed progenitors and myeloid cells from the same xenografts. These were sequenced on an Illumina NovaSea 6000 platform; BAM files are provided. Samples from 3 conditions were sequenced for each cell type; 3 chromatin accessibility runs and 9 gene expression runs are provided.

  Dataset EGAD50000002328

• Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer

  The utility of circulating tumour DNA (ctDNA) for longitudinal tumour monitoring in pancreatic ductal adenocarcinoma (PDAC) has not been explored beyond mutations in the KRAS proto-oncogene. We aim to characterise and track patient-specific somatic ctDNA variants, to assess longitudinal changes in disease burden and explore the landscape of actionable alterations.

  Study EGAS00001005981

• Long-read sequencing for cell-free DNA analysis (mouse)

  In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced with the two platforms.

  Study EGAS00001006329

• Cancer sequencing for somatic variant calling

  This dataset includes WES and RNAseq for 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy tissues, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems.

  Study EGAS00001007101

• H3K27ac/H3K27me3 landscape of medulloblastoma

  We profiled 111 patient medulloblastoma primary tumor samples by bulk RNA-seq (19 samples), 27ac (98 samples) / 27me3 (61 samples) ChIP-Seq, WGS (4 samples) and 27ac hichip (8 samples). Submitted data consists of data generated from previously unpublished tumors as well as complementary data for data sets already published for identical medulloblastoma tumors (ex: 27me3 ChIP-Seq and RNA-Seq data submitted for a tumor with publicly available WGS data). The raw fastqs and hg19 aligned RNA-Seq bams are provided.

  Dataset EGAD00001009709

• IntEnd study

  Formalin-fixed, paraffin-embedded samples from 643 colorectal adenomas collected in different hospitals in Norway, from which DNA was extracted, were analysed for DNA copy number alterations. Some adenomas had more than one block (n=42), thus 643 individuals, 685 blocks. Low-coverage whole genome sequencing was run in all samples. For 529 individuals all the clinical information was available. A subset was matched for follow-up time, age and sex in a nested case-control approach (n=366; cases - individuals who developed later on CRC; controls - individuals who did not develop CRC within the same follow-up time).

  Dataset EGAD00001010119

• CCA ChIP-seq data (63 CCA, 8 normal, 19 cell-line)

  Fastq files for H3K27ac ChIP-seq (with matched input-DNA control) for 63 CCAs, 8 normal bile duct tissues, 16 CCA cell-lines (including replicates), and 3 normal cholangiocyte cell-lines (including replicates). Library prep was performed with the NEBNext ChIP-seq library preparation kit. Each library (including matching input DNA) was sequenced to an average depth of 20 to 30 million raw reads on Illumina HiSeq4000 sequencer, with paired-end sequencing (except for 3 normal bile tissues done with single-end sequencing).

  Dataset EGAD00001012103

• Targeted_Pulldown_Validation_of_mutations_found_in_whole_genome_sequencing

  This experiment is to inform us of the validity of using pre-made library material to perform a bespoke pulldown experiment to validate the mutations found between the whole genome sequencing of the DNA from the same individuals cancer and normal material. This is to identify the valid and informative mutations in cancer genomes.

  Study EGAS00001000260

• The_effects_of_chemotherapy_and_radiation_in_human_oesophageal_epithelium__low_input

  Human oesophagus is a patchwork of competing mutant clones. We wish to see how this patchwork is altered under the extreme selection pressures of chemotherapy and radiotherapy both individually and combined. We will sequence 0.25mm diameter punch biopsies from patients who have undergone chemotherapy and radiotherapy to assess how the mutational landscape has changed.

  Study EGAS00001007416

• The_effects_of_chemotherapy_and_radiation_in_human_oesophageal_epithelium

  Human oesophagus is a patchwork of competing mutant clones. We wish to see how this patchwork is altered under the extreme selection pressures of chemotherapy and radiotherapy both individually and combined. We will sequence 2mm2 contiguous pieces of oesophageal epithelium from patients who have undergone chemotherapy and radiotherapy to assess how the mutational landscape has changed.

  Study EGAS00001007417

• Progressive multifocal leukoencephalopathy (PML)

  We generated RNAseq, ATACseq, Multiomics and CITEseq for patients with Progressive multifocal leukoencephalopathy (PML) to profile the chromatin accessibility, transcriptional profiles and surface proteins at single-cell level.

  Study EGAS50000000139

• Human TRIM24-MET fusion HGG RNA-seq

  Human RNA-seq data for TRIM24-MET fusion tumor primary samples and patient/PDOX-derived cell lines. Cells were treated with 0.1% DMSO or EC90 of MET inhibitors (capmatinib, cabozantinib, crizotinib) for 4 hours. BAM files containing aligned (and unaligned) reads to hg19 are provided.

  Dataset EGAD50000000194

• DAC for "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis"

  DAC for the data of "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis" with: • Holger Sültmann • h.sueltmann@dkfz.de • German Cancer Research Center (DKFZ) • Ann-Kathrin Daum • a.daum@dkfz.de • German Cancer Research Center (DKFZ)

  Dac EGAC50000000076

• CITE-seq data of six CK-AML patient samples

  We performed cellular indexing of transcriptomes and epitopes (CITE-seq) of six primary leukemia samples from CK-AML patients. The dataset contains BAM files for each individual sample (D1922 and R0836) or for the hashed pool (HIAML47-HIAML85, P9D-P9R)

  Dataset EGAD50000000633

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 1), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000917

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 2), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000921

• Dataset for "HPV integration induces gene fusions" (Illumina)

  Illumina whole-genome sequencing data for "HPV integration induces gene fusions" We performed short read whole-genome sequencing of five HPV+ head and neck cancer samples using Illumina. The reads are submitted in bam or fastq file format.

  Dataset EGAD50000001305

• Genetic Analysis of Tuberous Sclerosis Complex (TSC) Hypomelanotic Macules

  In this study we searched for mutations in the TSC1 and TSC2 genes in cultured melanocytes from individuals with the genetic disease Tuberous Sclerosis Complex.

  Study phs001236

• WGS data for Pancreatic Cancer samples (misc.)

  WGS data for pancreatic cancer samples. These are miscellaneous samples which are part of a tandem duplicator phenotype paper (Farooq et al, NPJ Precision Oncology, 2025). The dataset includes tumour and normal BAM files sequenced on Illumina NovaSeq 6000 and aligned against GRCh38 (n=7 tumour/normal pairs).

  Dataset EGAD50000001833

• Sequencing dataset for the Predictive Endocrine ResistanCe Index (PERCI) in Breast Cancer cases

  Sequencing dataset for the Predictive Endocrine ResistanCe Index (PERCI) in Breast Cancer cases of the WSG-ADAPT trial (NCT01779206). The Oncomine Comprehensive v3 assay (ThermoFisher) and a customized amplicon-based NGS-Panel (DERv2) was performed.

  Dataset EGAD50000001595