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• 10x Genomics BCR Sequencing

  BCR sequencing done with 10x Genomics V(D)J kit + platform for the paper: Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma. Dataset contains paired FASTQ files for 35 samples, each was processed with the 10x Genomics V(D)J kit to obtain the sequence of the B-cell receptor sequence.

  Dataset EGAD50000001373

• Genetic screening of GPI-anchor protein synthesis

  This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001001928

• RNA-seq analysis of TGF-β-induced transcriptional changes in 19TT cancer-associated fibroblasts

  The dataset contains 6 samples, three biological replicates for vehicle-treated 19TT cells, and three biological replicates for TGF-β-treated 19TT cells. The dataset was generated by the next generation high throughput sequencing. Strand specific transcriptome library construction is completed by enriching mRNA from total RNA, sequenced by DNBSEQ high throughput platform.

  Dataset EGAD50000001350

• scRNA-seq raw data

  This dataset contains scRNA-seq fastq files (trimmed for quality and adapters using Trim Galore) for 3739 intestinal plasma cells of known or unknown antigen specificities from in total 12 individuals (4 untreated coeliac disease patients, 3 treated coeliac disease patients, 5 controls). The data was generated using the Smart-seq2 protocol and sequenced on the Illumina NextSeq500 platform with 75 bp paired-end reads.

  Dataset EGAD00001006436

• Spatially resolved cellular and molecular drivers of cardiac remodelling in healthy and failing human hearts: Adult RNA (2025-07-31)

  Cell Atlas of the diseased human heart. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2025-07-31.

  Dataset EGAD00001015668

• Genome Sequencing of Hepatocellular Carcinoma at The Human Genome Sequencing Center of Baylor College of Medicine (HGSC-BCM)

  Hepatocellular carcinoma (HCC) accounts for 85-90% of primary liver cancers. We have focused on three major HCC etiologies:hepatitis C virus (HCV), hepatitis B virus (HBV), and nonviral causes. The onset and progression of cancer is driven by extensive rearrangement and mutation of the genome. We combined our capability to capture and enrich exome DNA with the next generation sequencing capacity to allow us to detect and characterize the somatic mutation profile of patients with HCC. Patient samples were collected by the Liver Center, Division of Abdominal Transplantation in the Baylor College of Medicine Department of Surgery. Sequencing of HCC is one of the NHGRI Center Initiated Projects in progress in the Human Genome Sequencing Center at Baylor College of Medicine.

  Study phs000509

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): Large Scale Flu Surveillance Study (LSFS)

  The purpose of this study was to better understand behavioral and physiological functioning in relation to recent self-reported influenza and influenza-like-illness (ILI), including coronavirus disease (COVID-19). Over 65,000 Achievement members responded to a weekly one-click survey asking if they had experienced ILI within the previous 7-day period. If they responded no, they were given the option to complete a survey about their risk factors and behavior. If they responded yes, they were given the option to complete a survey asking about the specifics of the incident. Participants were also asked to sync their wearable activity trackers and health apps in order for researchers to better understand changes in behavioral and physiological outcomes related to self-reported ILI experiences.DOI: https://rapids.ll.mit.edu/10.57895/fkth-d352

  Study phs002539

• Melanoma Brain Metastasis Single-Cell RNA Sequencing Atlas

  Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma, yet our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBM (scRNA-seq n=5; snRNA-seq n=17) and 10 extracranial melanoma metastases (ECM; all snRNA-seq), and matched spatial single-cell transcriptomics (n=16) and T cell receptor (TCR)-seq (n=5). Key observations were validated in matched bulk RNA- and ATAC-seq of isogenic MBM/ECM cell culture models (n=24; including triplicates (labeled as *-A, -B and -C) of 4 MBM- and 4 ECM-derived patient cell lines with 2 matched pairs). This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.

  Study phs002944

• Whole genome sequencing of human induced pluripotent stem cells derived from 5 type I cyctic biliary atresia patients

  We have successfully generated a panel of human induced pluripotent stem cells (hiPSCs) from five Japanese patients carrying type I cystic biliary atresia (BA). These hiPSC lines have exhibited characteristics of self-renewal and pluripotency. These cells held normal karyotypes mostly, but one of them carried hemizygous deletions, of which clinical significance is unknown yet. Whole genome sequence analysis indicated that some of the mutations or single nucleotide polymorphisms (SNPs) commonly found in these patients are related to hepatobiliary abnormality. Given the limited understanding of the molecular pathogenesis of cystic BA, attributed to unknown factors of genetic and environmental causes, these cellular resources will be instrumental in replicating disease phenotypes and in the advancement of novel therapies for this condition.

  Study JGAS000765

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Study EGAS50000001327