3743 results for "RNA AND sequencing OR transcriptome"

in 22.72 milliseconds.

• Depth of Response Correlates with Improved Outcomes for Early Interception in a High-Risk Smoldering Multiple Myeloma Clinical Trial Using the Combination of Ixazomib, Lenalidomide, and Dexamethasone

  Early treatment of patients with high-risk smoldering myeloma (HRSMM) has been shown to delay progression to multiple myeloma (MM), but not all patients respond well. Identifying biological predictors of response and resistance to treatment can help optimize treatment selection for patients and improve outcomes. Here, we investigate tumor and immune biomarkers of response to ixazomib, lenalidomide, and dexamethasone treatment (I-PRISM study) that can be measured at diagnosis. We performed single-cell RNA sequencing (scRNAseq), coupled with B cell receptor and T cell receptor sequencing, on CD138+ tumor and CD138- immune cells, respectively, from the bone marrow of 20 patients enrolled in the I-PRISM study.

  Study phs003827

• Genomic profiling of IBC

  We collected matched pretreatment blood and tumor samples from 19 patients with primary TN-IBC enrolled in a phase II clinical trial (NCT02876107). Patients were treated with neoadjuvant chemotherapy (NAC) or the anti-EGFR antibody panitumumab (PmAb) plus NAC (PmAb/NAC). We conducted whole-exome sequencing, RNA sequencing, and CIBERSORT analyses for these TN-IBC samples and compare the genetic and molecular profiles with similarly analyzed stage III TN-non-IBC patient samples. We also compared the genetic and molecular characteristics of TN-IBC in patients who had a pathologic complete response (pCR) to NAC or PmAb/NAC treatment, a suitable surrogate endpoint for IBC, with those who did not have pCR (non-pCR).

  Study EGAS00001007520

• Single cell transcriptional characterization of human megakaryocyte lineage commitment and maturation

  Single cell RNA-sequencing of sternal bone marrow reciding Hematopoietic Stem Cells (HSCs) and Megakaryocytes (MKs) from individuals undergoing elective open heart valve replacement. HSCs were defined as Lineage-, CD34+, CD38-, CD45RA-, CD90+, CD49f+ cells. MKs where CD41a+, CD42b+ and ploidy was determined with Hoechst. A sternal bone marrow scraping was taken directly following median sternotomy using a Volkmann’s spoon. The sample was collected into an EDTA Vacutainer tube containing 1.8mg/ml EDTA. 4mL of Dulbecco’s phosphate buffered saline (PBS, Sigma) containing 10% human serum albumin (HSA, Gemini Bio Products) was added and the whole volume was resuspended by pipetting 2-3 times. The sample was then put on metallic thermal beads (ThermoFisher Scientific) at a temperature between 0-4°C and transported to the University of Cambridge for further processing. For HSC isolation the cells were stained with the following antibody cocktail: PECy5 conjugated anti-lineage specific antibodies: CD2 (BD), CD3 (BD), CD10 (BD), CD11b (BD), CD11c (BD), CD19 (BD), CD20 (BD), CD56 (BD), biotinylated CD42b (Pab5, NHS Blood and Transplant, International Blood Group Reference Laboratory [IBGRL]), biotinylated GP6 (Pab5, NHS Blood and Transplant, International Blood Group Reference Laboratory [IBGRL]) used in combination with PECy5 conjugated streptavidin (Biolegend). Alexa Fluor 700 conjugated anti-CD34 (BD), PerCP-Cy5.5 conjugated anti-CD38 (BD), Pacific Blue conjugated anti-CD45RA (Invitrogen), PECy7 conjugated anti-CD90 (BD),PE conjugated anti-CD49f (BD). After staining cells were kept at 4°C before sorting using a FACS Aria Fusion flow sorter (BD). Single HSCs defined as Lineage-, CD34+, CD38-, CD45RA-, CD90+, CD49f+ cells were sorted by FACS directly into individual wells of a 96-well plate. Index sort data was collected for each single cell. For MK isolation the cells were stained for surface MK markers with mouse anti-human CD41a APC conjugated antibody (BD) and mouse anti-human CD42b PE conjugated antibody (BD) and for ploidy analysis with 1ug/ml Hoechst 33342 (Invitrogen). After incubation at 37°C for 30 minutes, the cells were kept at 4°C before sorting using a FACS Aria Fusion flow sorter (BD). Single cells and MK pools of 20 cells were sorted by FACS according to ploidy level using a 100uM nozzle directly into individual wells of a 96-well plate. cDNA synthesis and poly(A) enrichment was performed following the G&T-seq protocol (Macaulay et al. 2015), a variation of the Smart-seq2 protocol1. ERCC spike-in RNA (Ambion) was added to the lysis buffer in a dilution of 1:4,000,000.

  Dataset EGAD00001006677

• Genomic and epigenomic study of Japanese renal cell carcinoma including WGS, RNA-seq, ATAC-seq, and methyl-seq

  We performed whole-genomic and transcriptomic sequencing of more than 100 Japanese renal cell carcinoma (RCC) cases, including clear cell RCC, papillary RCC, chromophobe RCC, and TFE3-translocated RCC. In addition, we conducted epigenome sequencing analyses: the assay for transposase-accessible chromatin sequencing (ATAC-seq) and enzymatic methyl sequencing.

  Study EGAS00001006919

• DNTR sequencing data of paediatric acute lymphoblastic leukemia

  This study used the DNTR-seq method in leukaemia samples to profile the whole-genome and mRNA jointly in single cells. Direct tagmentation is used in a collection of single-cell whole genome sequencing (scWGS) methods, including DNTR-seq, which provide high quality data at ultra-low to low coverage. The overall goal was to characterize the genetic and transcriptional heterogeneity of cancer samples. To infer clonal structure and evolutionary history, copy number analysis based workflows were implemented. Bone marrow mononuclear cells from pediatric acute lymphoblastic leukemia samples were FACS sorted into 384 plates to generate the DNA and RNA profiles.

  Study EGAS50000001247

• University of Washington Cerebrospinal Fluid Biomarker Study for Parkinson disease

  There is a clear need to develop biomarkers for Parkinson disease (PD) diagnosis and monitoring disease progression. In this study we evaluated cerebrospinal fluid (CSF) proteins, which are known to be critically involved in PD or identified in our preliminary profiling studies, aptamers, and RNAs as potential PD biomarkers. Access to subjects for this study was via the Pacific Northwest Udall Center (PANUC) and the Alzheimer's Disease Research Center (ADRC) at the University of Washington and Oregon Health and Sciences University (OHSU). Using CSF samples from 30 well-characterized patients with PD and 30 age-, sex-matched healthy controls, we prepared RNA seq libraries and performed deep sequencing of all RNA species, including small and long RNA, mRNAs, noncoding RNAs and differentially spliced transcripts. We then tried several methods for RNAseq data analysis to optimize our analysis pipeline. We identified a total of 3381 transcripts corresponding to 182 long intergenic RNAs (LincRNAs), 11 microRNAs (miRNAs), 2861 protein-coding transcripts, 200 pseudogenes and 127 antisense RNAs; some of them were differentially expressed between PD and control groups. Selected differentially expressed RNAs have been validated in the same set of CSF samples using real-time PCR (RT-PCR). Further validations in independent, larger cohorts of samples are still ongoing. Our results obtained so far suggested that CSF proteins and RNAs could be used as good indexes for PD diagnosis and disease severity/progression. This study is a part of the NIDDS-funded Parkinson's Disease Biomarkers Program (PDBP).

  Study phs000901

• Detection of Gene Fusions using Targeted Next-Generation Sequencing

  Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).

  Dataset EGAD00001006913

• Whole-genome sequencing of rhabdomyosarcoma tumouroids (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumoroids data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015707

• Whole Genome-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015709

• Whole Genome-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015716

• The Finland-United States Investigation of NIDDM Genetics (FUSION) Tissue Biopsy Study

  The Finland-United States Investigation of NIDDM Genetics (FUSION) study is a long-term effort to identify genetic variants that predispose to type 2 diabetes (T2D) or that impact the variability of T2D-related quantitative traits (QTs). Most of the variants associated with T2D and related traits (glucose and insulin, anthropometrics, lipids) through genome-wide association studies (GWAS) occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Regulatory element activity is often tissue-specific, which further complicates discovery of the causal/functional variation. Therefore, there is a critical need to identify the appropriate cell type, regulatory elements, target genes, and causal variants(s) in T2D-relevant tissues. We hypothesize that a subset of T2D and related variants alter gene expression regulation in skeletal muscle and adipose tissue - two major insulin target tissues and play key roles in insulin resistance. To that end, our study contains a comprehensive survey of genomics, epigenomics and transcriptomics in skeletal muscle and adipose tissue from individuals with glucose tolerance categories ranging from normal to T2D.For this FUSION Tissue Biopsy Study, we obtained RNA-Seq, microRNA (miRNA)-Seq, and DNA methylation (methyl)-Seq data on biopsy samples from 331 individuals from across the range of glucose tolerance: 124 normal glucose tolerance (NGT), 77 impaired glucose tolerance (IGT), 44 impaired fasting glucose (IFG), and 86 newly-diagnosed T2Ds. Participants completed two study visits, two weeks apart. First visits comprised most of the clinical phenotyping, including four-point OGTT (fasting, and 30, 60, and 120 minute post-load); BMI, WHR; lipids; blood pressure; and many other variables. Participants also completed FUSION health history, medication, and lifestyle questionnaires. On the second visit, we obtained ~250mg vastus lateralis skeletal muscle, ~750mg abdominal subcutaneous adipose, and a ~5x15mm section of abdominal skin. Visits were completed in March 2013. RNA isolation is ongoing in the Collins laboratory at the NIH, RNA and miRNA sequencing at the NIH Intramural Sequencing Center (NISC), and genotyping at the Center for Inherited Disease Research (CIDR). Individual-level data is available here for the 306 individuals who consented to data deposit. To focus on evaluation of gene expression and its regulation in skeletal muscle, we analyzed mRNA extracted from vastus lateralis skeletal muscle obtained from 271 of the 331 individual subjects from Finland, along with genome-wide genotypes. Individual-level data is available here for the 250 subjects who consented to the use of their data.Release phs001048.v2.p1 adds muscle data for an additional 42 subjects and data from adipose tissue for 276 subjects. Total RNA was isolated using Trizol extraction in the Collins laboratory at the NIH. The mRNA was poly-A selected, 24-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol and RNA sequencing was performed on HiSeq2000 sequencers using 101bp paired-end reads at NISC. miRNA libraries were prepared from total RNA from 296 muscle and 270 adipose samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. Data for 272 muscle and 251 adipose samples are available here for individuals with consent for data deposit. DNA was extracted from blood in the Collins laboratory, and genotyping on the Illumina Omni2.5M array was performed at CIDR. Genotypes were imputed using the HRC 2016 reference panel. In order to assess regions of open chromatin in skeletal muscle, we obtained muscle tissue from a commercial provider to perform ATAC-seq; these samples were sequenced at the University of Michigan DNA Sequencing Core.Release phs001048.v3.p1 adds single-nucleus (sn) RNA-seq and ATAC-seq data in 287 skeletal muscle samples out of the original 331 individuals. Individual-level data is available here for the 265 subjects who consented to the use of their data. The frozen tissue biopsy samples were processed in ten batches, each consisting of 40-41 samples. These batches were organized using a randomized block design to protect against experimental contrasts of interest including cohort, age, sex, BMI among others. Samples in each batch were pulverized, pooled together followed by nuclei isolation. The nuclei were processed on the 10X Genomics Chromium platform separately for snATAC-seq and snRNA-seq (v. 3.1 chemistry for snRNA-seq).Release phs001048.v4.p1 adds additional phenotypes and provides some corrections to several previous phenotypes.

  Study phs001048

• NINDS Deep Sequencing for the Detection of Viral Sequences in Primary Progressive Multiple Sclerosis Brains

  Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples (n = 7) from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed, and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue (Chan et al., 2014). Data from the primary progressive multiple sclerosis (PPMS) brain specimens (n = 14) and Normal Control brain specimens (n = 14) are also submitted here. All the subjects studied here (encephalitis, PPMS, and controls) were selected from existing collections at the Rocky Mountain and UCLA brain banks. These selections were performed by the directors at the two centers (Dr. Corboy at RM and Nagra at UCLA) based on clinic information provided at the time of collection. All the specimens are from deidentified deceased individuals. The submitting investigators have no identifying information on any of these subjects. To avoid confusion, the dbGaP Subject IDs are identical to the brain bank identifying numbers.

  Study phs000715

• COVID-19 Multiomics Atlas

  We provide a single-nuclei RNA-sequencing (snRNA-seq) dataset derived from four COVID-19 patients, generated using the 10x Chromium Next GEM Single Cell v3.1 kit. For our study, these were integrated with snRNA-seq data with 12 publicly available sc/snRNA-seq datasets, comprising organ donor lung samples (n=89) and COVID-19 lung tissue samples (n=51).

  Dataset EGAD00001015602

• Phase 2 Study of Nivolumab and Entinostat in Unresectable or Metastatic Cholangiocarcinoma and Pancreatic Adenocarcinoma

  The study was a single-center, open-label, phase II trial (registration no. NCT03250273) designed to evaluate the efficacy of entinostat in combination with nivolumab in patients with advanced pancreatic ductal adenocarcinoma (PDAC). The aim was to assess the objective response rate using RECIST v1.1 criteria as the primary endpoint. A total of 27 patients with advanced PDA were enrolled from November 2017 to November 2020. Their treatment involved a 14-day lead-in with entinostat monotherapy, followed by a combination with nivolumab. The study utilized several molecular technologies to assess immune profiles and tumor microenvironment (TME) changes: high-dimensional mass cytometry by time of flight (CyTOF), Luminex for chemokine analysis in plasma, multiplexed immunohistochemistry (mIHC), image cytometry-based quantification, bulk RNA sequencing analysis. The objective response rate (ORR) was 11% with three patients showing a partial response (PR). The median duration of response was 10.2 months. Grade ≥ 3 treatment-related adverse events (TRAEs) occurred in 63% of patients, with the most common being decreased lymphocyte count, anemia, hypoalbuminemia, and hyponatremia. Gene expression analysis showed an enrichment in inflammatory response signaling pathways with the combination treatment. RNA sequencing data with clinical and demographic patient information will be available through dbGaP. For expression summaries, please refer to GEO submission GSE248014.

  Study phs003615

• Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

  Background Single-cell RNA sequencing (scRNAseq) is a powerful tool for studying complex biological systems, such as tumour heterogeneity and tissue microenvironments. However, the sources of technical and biological variation in primary solid tumour tissues and patient-derived mouse xenografts for scRNAseq, are not well understood. Here, we used low temperature (6°C) protease and collagenase (37°C) to identify the transcriptional signatures associated with tissue dissociation across a diverse scRNAseq dataset comprising 128,481 cells from patient cancer tissues, patient-derived breast cancer xenografts and cancer cell lines.Results We observe substantial variation in standard quality control (QC) metrics of cell viability across conditions and tissues. From FACS sorted populations gated for cell viability, we identify a sub-population of dead cells that would pass standard data filtering practices, and quantify the extent to which their transcriptomes differ from live cells. We identify a further subpopulation of transcriptomically “dying” cells that exhibit up-regulation of MHC class I transcripts, in contrast with live and fully dead cells. From the contrast between tissue protease dissociation at 37°C or 6°C, we observe that collagenase digestion results in a stress response. We derive a core gene set of 512 heat shock and stress response genes, including FOS and JUN, induced by collagenase (37°C), which are minimized by dissociation with a cold active protease (6°C). While induction of these genes was highly conserved across all cell types, cell type-specific responses to collagenase digestion were observed in patient tissues. We observe that the yield of cancer and non-cancer cell types varies between tissues and dissociation methods.Conclusions The method and conditions of tumour dissociation influence cell yield and transcriptome state and are both tissue and cell type dependent. Interpretation of stress pathway expression differences in cancer single cell studies, including components of surface immune recognition such as MHC class I, may be especially confounded. We define a core set of 512 genes that can assist with identification of such effects in dissociated scRNA-seq experiments.

  Study EGAS00001003753

• Measuring the level of relatedness between NGS datasets

  Sequencing technologies are providing increasingly detailed insight in genetic makeup are paving their way into molecular diagnostics. The field will benefit from rigorous and bias-free measures for the quality of sequence data and for the proper representation of the complexity of the original samples. While current methodologies rely on the availability of a well-characterized reference genome, we propose kMer profiling for alignment-free assessment of the quality, comparability, and complexity of sequencing datasets. We show that kMer detects technical artefacts such as high duplication rates, library chimaeras, and differences in library preparation protocols in whole-genome, whole-exome, and RNA sequencing data. Additionally, it successfully captures the complexity and diversity of microbiomes. Thus, kMer allows for a robust evaluation of the quality and complexity of sequencing data without relying on any prior information and opens the way to a more reliable biological reasoning.

  Study EGAS00001000600

• Developing Targeted Therapy for Patients with Multiple Myeloma and Gain or Amplification of Chr1q (1q+)

  Multiple myeloma (MM) frequently presents with gain or amplification of chr1q (1q+), which is associated with inferior response to treatment and poor outcomes. To develop targeted therapy for MM with 1q+, we leveraged external and in-house dependency screens and drug screens, along with single-cell sequencing of patient tumors with subclonal 1q+. We demonstrated that MM with 1q+ exhibits higher sensitivity to MCL1 and PI3K inhibitors, which may be synergistic and act through established and novel mechanisms. Two human MM cell lines with 1q+, KMS12BM and KMS11, were profiled with either single-cell RNA-sequencing (scRNA-seq) alone (KMS12BM, KMS11) or both scRNA-seq and whole-genome sequencing (WGS; KMS12BM) to understand the factors that determine response to MCL1 and PI3K inhibitors and how these inhibitors work.

  Study phs003886

• Egyptref: An integrated personal and population-based Egyptian genome reference

  North African individuals are not represented in current genetic data sets. To address this issue, we generated an integrated personal and population-based Egyptian genome reference called Egyptref. Towards this end, we performed a human de novo assembly of an Egyptian individual using long PacBio reads (99x genome coverage) and polished it using Illumina short reads (90x). Variants were phased using 10x Genomics linked reads (80x). This personal genome was complemented with whole genome sequencing-based variant data of 109 further Egyptians and mitochondrial haplogroups from mtDNA sequencing of 326 further Egyptians (of which 100 individuals from EGAD00001001372/EGAD00001001380) to obtain a population-based genome. We used Egyptref for assessing the impact of genetic variation, e.g. by integration of blood RNA sequencing data of the assembly individual.

  Study EGAS00001004303

• Liver biopsy derived induced pluripotent stem cells provide an unlimited supply for the generation of patient-specific hepatocyte-like cells

  Background: Hepatocyte-like cells (HLCs) differentiated from induced pluripotent stem cells (iPSCs) have emerged as a promising cell culture model to study metabolism, biotransformation, viral infections and genetic liver diseases. However the derivation of iPSCs is restricted by ethical and procedural constraints. Furthermore, incomplete HLC differentiation remains a major challenge. iPSC may carry-on a tissue of origin dependent expression memory influencing iPSC differentiation into different cell types. If liver derived iPSCs (Li-iPSCs) maintain a liver specific gene expression profile is not known. It is also not known, if Li-iPSCs would allow the generation of more fully differentiated HLCs.Methods: Primary liver cells (PLCs) were expanded from liver needle biopsies and reprogrammed into Li-iPSCs using a non-integrative Sendai virus-based system. Li-iPSCs were differentiated into HLCs using established differentiation protocols. The HLC phenotype was characterized at the protein, functional and transcriptional level. RNA sequencing data were generated from the originating liver biopsies, the Li-iPSCs, fibroblast derived iPSCs, and differentiated HLCs, and used to characterize and compare their transcriptome profiles.Results: PLCs were obtained from small pieces of liver biopsies and could be reprogrammed into Li-iPSCs. Li-iPSCs indeed retain a liver specific transcriptional footprint. Li-iPSCs can be propagated to provide an unlimited supply of cells for differentiation into Li-HLCs. Similar to HLCs derived from fibroblasts, Li-HLCs could not be fully differentiated into hepatocytes. Relative to the originating liver, Li-HLCs showed lower expression of liver specific transcription factors and increased expression of genes involved in the differentiation of other tissues.Conclusions: PLCs and Li-iPSCs obtained from small pieces of human needle liver biopsies constitute a novel unlimited source for the production of HLCs. Despite the preservation of a liver specific gene expression footprint in Li-iPSCs, the generation of fully differentiated hepatocytes cannot be achieved with the current differentiation protocols.

  Study EGAS00001002676

• Single-cell RNA sequencing of human skin tumors (BCC, SCC and Melanoma)

  Cancer-associated fibroblasts (CAFs) play a key role in cancer progression and treatment outcome. Here, we elucidate the yet unresolved intra-tumoral CAF variety in three skin cancer types at molecular and spatial single-cell resolution in a large cohort. We show that two out of three CAF subtypes contribute to tumor immune surveillance with distinct mechanisms. Matrix CAFs (mCAFs) ensheath tumor nests and synthesize extracellular-matrix to prevent T cell invasion. Immunomodulatory CAFs (iCAFs), which express proinflammatory and immunomodulatory factors, are only detected in high abundance in aggressive tumors. Strikingly, iCAFs but not tumor cells are (apart from immune cells) the exclusive cell type producing chemokines and, thus, play a key role in immune cell recruitment and activation. Mechanistically, we show that cancer cells transform adjacent healthy fibroblasts into cytokine-expressing iCAFs, which subsequently recruit immune cells and modulate the immune response. In conclusion, targeting CAF variants holds promise for improved efficacy of immunotherapy.

  Study EGAS50000000365

• Transcriptomic Profiling of Patient Derived Alternative Lengthening of Telomeres (ALT) and Non-MYCN-Amplified Neuroblastoma Cell Lines

  Patient derived neuroblastoma cell lines are excellent tools to study biology of the disease. While many previous studies sequenced neuroblastoma cell lines, there are very few ALT and non-MYCN-amplified neuroblastoma cell lines that were sequenced previously. Here, we present raw RNA sequencing data for 3 ALT (CHLA-90, SK-N-FI, COG-N-515) and 8 non-MYCN-amplified telomerase positive (CHLA-171, Felix, COG-N-579h, COG-N-615, COG-N-618h, COG-N-619h, COG-N-708h, COG-N-709) neuroblastoma cell lines. Additionally, gene expression data are provided as a supplement files.

  Study phs002421

• High-resolution profile of neoantigen-specific TCR activation links moderate stimulation to increased resilience of engineered TCR-T cells

  Neoantigen-specific T cell receptors (neoTCRs) promise safe, personalized anti-tumor immunotherapy. Previously, we identified diverse neoTCRs restricted to different neoantigens in a melanoma patient. In this work, we now combined single-cell TCR- and RNA-sequencing after neoantigen-specific restimulation of peripheral blood-derived CD8+ T cells of this patient. We detected novel neoTCRs with specificity to the previously detected neoantigens and observe a heterogeneous spectrum of TCR-intrinsic activation patterns in response to a shared neoepitope ranging from previously detected higher frequent neoTCRs with moderate activation to rare ones with initially stronger activation.

  Study EGAS50000000600

• Expression quantitative trait loci analysis using human immune cells in a Japanese population

  Recent evidence suggests that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner. Therefore, it is reasonable to expect that cell-specific expression quantitative trait loci (eQTL) analysis can identify the candidate causal mechanisms of complex diseases (an eQTL is a variant whose polymorphism affects gene expression). We fractionated peripheral blood from 105 healthy Japanese volunteers into five major immune cell subsets (CD4+ T cells, CD8+ T cells, B cells, NK cells, and monocytes). We quantified gene and exon expression by RNA sequencing, and tested associations with neighboring common variants (MAF ? 0.05).

  Study JGAS000085

• RNAseq profile of monomorphic epitheliotropic intestinal T-cell lymphoma and enteropathy associated T-cell lymphoma

  Background : Enteropathy-associated T-cell lymphoma (EATL) and monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL) are aggressive malignancies with limited treatment options and poor prognosis. Our research on MEITL has uncovered its genetic portrait including hallmark SEDT2 mutations, expanded its pathological spectrum, and identified molecular biomarkers influencing patients’ outcome. In this study, we aimed to establish and clarify the similar and diverging features of EATL. Methods : A large combined cohort of patients with EATL (n=30) and MEITL (n=52) was assembled and tumor samples were used for whole-exome and RNA sequencing profiling.

  Study EGAS50000001125

• RNAseq of MCL cell lines

  This study profiles the transcriptomic response of the Mino-VEN-R and Jeko-BTK-R mantle cell lymphoma (MCL) cell lines to pirtobrutinib (PBN) treatment using bulk RNA sequencing. Mino-VEN-R models drug-tolerant persister (DTP) cells that arise during exposure to non-covalent BTK inhibitors. Building on our recent findings that DTP cells undergo metabolic and phenotypic state transitions governed by TCA cycle reprogramming, this dataset aims to capture gene expression changes associated with treatment-induced plasticity. The results contribute to a broader multi-omic framework exploring mechanisms of resistance and therapeutic vulnerability in MCL.

  Study EGAS50000001087

• Characterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer

  Our study provides insight into molecular alterations in HN tissues within the affected breast and offers a greater understanding of the spatial implications of these aberrations. This was achieved by performing a comprehensive analysis of RNA sequencing data and proteomic profiles from breast cancers (n=19) and their matched HN tissues (n=38), healthy breast from cosmetic reduction mammoplasty (RM; n=5), and risk reducing mastectomies (RR, n=5), with peritumoral samples excised at proximal (TP, <2 cm) and distal (TD, 5-10 cm) sites from the primary tumor.

  Study EGAS00001004510

• Exploring_the_heterogeneity_of_sarcoma_using_single_cell_sequencing_

  Multi region samples are collected from patients, with consent, immediately after resection of the tumour. Samples are digested and sorted using FACS as single cells into lysis buffer. Cells are then stored until further processing for G&T-seq. After sequencing, we will explore intra-tumour heterogeneity using computational approaches to integrate RNA and DNA data onto the tumour phylogeny 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/

  Study EGAS00001002866

• Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies unique proteotypes associated with patient outcomes

  Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide. Only a fraction of NSCLC harbour actionable driver mutations and there is an urgent need for patient-derived model systems that will enable the development of new targeted therapies. NSCLC and other cancers display profound proteome remodelling compared to normal tissue that is not predicted by DNA or RNA analyses. We generated NSCLC patient-derived xenografts (PDXs) that recapitulate the histology and molecular features of primary NSCLC. Here, we completed whole exome sequencing on 122 NSCLC PDXs.

  Study EGAS00001006068

• Juntendo Muscle Study (JMS)

  Skeletal muscle fiber type distribution has implications for human health, muscle function and performance. This knowledge has been gathered using labor intensive and costly methodology that limited these studies. This data was used to present a new method based on muscle tissue RNA sequencing data to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for larger number of individuals to be tested in a cost and labor efficient way. Muscle biopsies were taken from the vastus lateralis muscle of 23 human subjects from Japan. Samples were sequenced on the NextSeq® 500/550 (Illumina).

  Study EGAS00001006362

• Muscle SATellite cell study (MSAT)

  Skeletal muscle fiber type distribution has implications for human health, muscle function and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. This data was used to present a new method based on muscle tissue RNA sequencing data to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for larger number of individuals to be tested in a cost and labor efficient way. Muscle biopsies were taken from the vastus lateralis muscle of 39 Swedish male subjects. Samples were sequenced on the NextSeq® 500/550 (Illumina).

  Study EGAS00001006363

• Multiregional single cell RNA sequencing of human renal cell carcinoma

  The dataset comprises of 5' single cell RNA sequencing with TCR enrichment with 10x Genomics' Chromium technology of multiregional biopsies of human renal cell carcinomas. Biopsies from different tumour regions, the tumour-normal interface, normal kidney, normal adrenal, metastatic regions, peri-nephric fat, and peripheral blood were sequenced from 12 patients with kidney tumours.

  Dataset EGAD00001008030

• Preferential infiltration of distinct Vγ9δ2 T cells into Glioblastoma multiforme

  Glioblastoma multiforme (GBM), the most fatal CNS cancer, is highly infiltrative as a result of phenotypic alteration of cancer cells mainly driven by a mutual interaction among cancer cells, tumor-associated macrophages (TAMs) and other stromal cells. This work aims at characterizing GBM-infiltrating γδ T cells that may regulate the GBM tumor microenvironment and cancer cell gene expression. V(D)J repertoires of tumor-infiltrating and blood circulating γδ T cells from 4 patients were analyzed by NGS-based TCR sequencing. RNA gene expression profiling and immunostaining of cancer tissues were performed as well.

  Study EGAS00001002790

• Single Cell and Spatial Transcriptomic Profiling of Haemophilus ducreyi Infection

  We investigated the immune response in end-point pustules formed by Haemophilus ducreyi in volunteers using an experimental infection model. Six volunteers were infected in the skin of the upper arm at three sites with 41-85 CFU of H. ducreyi loaded on an allergy testing device; a sham-inoculated (e.g., wound) site was also performed. Five volunteers (4 men and 1 woman; 2 Asians and 3 Whites; aged 27-46 years) formed pustules 6-8 days post infection; 1 volunteer spontaneously resolved all sites. If a volunteer formed pustules, biopsies were performed to collect their pustule and wound sites. Biopsy pairs for all 5 pustule formers were subjected to single cell (sc) RNA-seq. Sequencing libraries were prepared using the 10X Genomics Single-cell 3' RNA-seq kit. Spatial transcriptomics was performed on biopsy pairs from 4 of the 5 pustule formers. Ten micron sections were placed on 10X Genomics Visium slides for fresh-frozen tissue, and libraries were prepared with the 10X Genomics Visium spatial 3' gene expression kit. All samples were sequenced on an Illumina NovaSeq 6000. Count tables were produced with CellRanger and SpaceRanger, respectively, and Seurat was used to analyze the data. We identified 13 major cell types by scRNA-seq; the proportion of some immune cell subsets was increased in pustules compared to wound sites. We also localized the major cell types within the tissue by using the scRNA-seq data to deconvolve the spatial transcriptomic data. The FASTQ files and count tables from CellRanger and SpaceRanger are provided.

  Study phs003754

• Single-Cell and Spatial Multi-Omics Highlight Effects of Anti-Integrin Therapy Across Cellular Compartments in Ulcerative Colitis

  This is a focused, nested case-control study within our larger cohort "Immunoprofiling of the Blood and Intestine and Creation of a Gut Cell Atlas". This sub-study is titled as "Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis”. We examined the impact of Vedolizumab (VDZ), an anti-integrin antibody therapy, on the cellular landscape of ulcerative colitis (UC). While VDZ is primarily recognized for its role in preventing lymphocyte migration to the gut, the extent of its influence on other cellular populations has not been fully characterized. We used single-cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to profile cells from both the blood and colon tissue samples. We pooled single-cell suspensions together before running scRNA-seq and CITE-seq, and subsequently deconvoluted the samples using the freemuxlet and demuxlet algorithms and variant call files (vcf) from bulk RNA-seq. This allowed us to assign cells to individual study subjects. We compared the cellular compositions of healthy individuals to those of UC patients undergoing treatment with VDZ or mesalamine (5-aminosalicylic acid/5-ASA). Our results revealed that VDZ induces significant changes in the variety and dynamics of mononuclear phagocytes within both the bloodstream and intestinal tissue, accompanied by subtle variations in lymphocyte populations. The dbGaP submission will provide raw sequencing data and participant phenotype data regarding disease and treatment status.

  Study phs003502

• A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer

  Background Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. Methods We combined immunohistochemistry (IHC) with RNA-sequencing and whole genome sequencing across a diverse spectrum of high-risk paediatric cancers to develop an alternative, expression-based signature associated with CD8+ T-cell infiltration of the TIME. Further, we explored transcriptional features of immune archetypes, T-cell receptor sequencing diversity, assessed the relationship between CD8+ and CD4+ abundance by IHC and deconvolution predictions, and assessed common adult biomarkers such as neoantigen load and TMB. Results A novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), was identified. Using this signature, we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. In addition, we showed that PD-L1 protein expression is poorly correlated with PD-L1 RNA expression and TMB and neoantigen load are not predictive of T-cell infiltration in paediatrics. Furthermore, deconvolution algorithms are only weakly correlated with IHC measurements of T-cells. Conclusions Our data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.

  Study EGAS00001007029

• Characterization of X Chromosome Inactivation Using Integrated Analysis of Whole-Exome and mRNA Sequencing

  This study of DNA and RNA sequencing of 5 parent-offspring trios is a single center study. The goal of this study is to characterize X chromosome inactivation (XCI) ratio in females using phased genomic variations obtained through whole genome or exome sequencing in trios, followed by allele-specific expression analysis of the phased, heterozygous alleles in the mRNA of the female offspring, and to apply this method to clinical diagnosis. The distribution of allele ratios across X obtained from mRNA sequencing allows for the estimation of X inactivation status of inherited X chromosomes, and the parameters of each parental allele distributions in the offspring's mRNA data can be used as determinants for XCI ratio. This approach was used to evaluate the contribution of skewed XCI ratio to phenotypic heterogeneity in an undiagnosed, mild neurological condition.

  Study phs000816

• Long-Read Sequencing to Identify Inherited Mutations Predisposing to Breast Cancer

  We aimed to detect deeply intronic mutations within genes linked to breast/ovarian cancer that are potentially under-reported in clinical testing due to technical limitations. Current DNA and RNA tests typically exclude these regions, which harbor many variants within complex repetitive sequences that short-read sequencing cannot align. By employing targeted long read sequencing together with recent in silico prediction tools, we assessed the implications of rare deep intronic variants in severely affected patients with breast, ovarian, and/or metastatic prostate cancer, who had previously tested negative using standard genomic or cDNA methods. Through this approach, we identified participants who carried deep intronic mutations in tumor suppressor genes, resulting in abnormal transcripts causing premature truncations and loss of gene function. This study underscores the potential of long read DNA and cDNA sequencing in enhancing mutation discovery efforts.

  Study phs003638

• Paired healthy & tumor organoid Biobank _B16PON

  Organoid cultures derived from colorectal adenomas. RNA and DNA was isolated from these cultures for genome wide profiling.

  Dataset EGAD00001008949

• Small RNA Contents of Extracellular Vesicles from Patients with Cognitive Decline

  In this proposal, we examined samples from living neurologically normal individuals (n=72), cognitively normal Parkinson's disease (PD; n=21), PD with mild cognitive impairment (PD-MCI; n=18), PD with dementia (PDD; n=23), and dementia with Lewy-bodies (DLB; n=18), Alzheimer’s disease (AD; n=33) and mild cognitive impairment (MCI, n=38). The main goal for this study was to assess the diagnostic utility of small RNA contents from extracellular vesicles (EVs) for the prediction of cognitive decline. Plasma samples were collected and the RNA from extracellular vesicles (EVs) was isolated using the Qiagen exoRNeasy kit, and the small RNA contents were sequenced using the PerkinElmer NextFlex kit (v2). While PD is typically thought of as a motor disorder, there are significant non-motor symptoms that can be devastating. One of the most common non-motor symptoms of PD is dementia (PDD). While PD subjects that develop dementia all have Lewy bodies, there is often co-pathology with tau and β-amyloid found at autopsy or by PET amyloid imaging; thus, subjects diagnosed with AD were also included in the study. The development of the category, mild cognitive impairment (MCI) in AD, and in PD, provides an opportunity to identify and examine a transitional state between normal aging and dementia; this is a patient population ideally suited for therapeutic intervention. Progress in the detection, validation, and standardization of molecular biomarkers from biofluids, such as extracellular RNAs (exRNAs), would be efficient and cost-effective aids in the assessment of disease progression, cognitive decline, and response to therapeutics. We have provided the raw fastq files for the sequencing data from each sample. We are also providing demographic information, as complete as we have for each person; including age, diagnosis, sex, and cognitive assessments.

  Study phs003300

• Mechanisms of Restoring T Cell Immunity after Cure of Chronic Viral Infection

  We analyzed hepatitis C virus (HCV)-specific T cells and non-specific memory T cell populations from 6 patients with chronic HCV infection receiving 12 weeks of direct-acting antiviral (DAA) therapy with aritaprevir/ritonavir/ombitasvir + dasabuvir + ribavirin. All patients were treated successfully. Peripheral blood mononuclear cells were obtained from blood draws right before treatment initiation (Pre-DAA) and 12 months after the end of treatment (Post-DAA). In each patient, HCV-specific cells were sorted using two different HCV multimers: One representing an epitope present in the circulating HCV genome and one epitope where the virus had escaped the T cell response and thus the corresponding T cells did not receive a TCR signal in vivo. Sorted specific T-cell populations and memory T cell subpopulations were analyzed by extracting RNA and performing RNA sequencing using the Smart-Seq2 protocol. A group of 8 patients with acute self-limited HCV infection (resolvers) were included as control representing natural control of infection. These patients were studied 24 weeks after their last detectable HCV viremia. Finally, we confirmed the data from chronically treated patients in a confirmatory cohort, consisting of 9 patients after successful antiviral treatment.

  Study phs002510

• PATL2 is a key actor of oocyte maturation whose invalidation causes infertility in women and mice

  The genetic causes of oocyte meiotic deficiency (OMD), a form of primary infertility characterised by the production of immature oocytes, remain largely unexplored. Using whole exome sequencing, we found that 26% of a cohort of 23 subjects with OMD harboured the same homozygous nonsense pathogenic mutation in PATL2, a gene encoding a putative RNA-binding protein. Using Patl2 knockout mice, we confirmed that PATL2 deficiency disturbs oocyte maturation, since oocytes and zygotes exhibit morphological and developmental defects respectively. PATL2's amphibian orthologue is involved in the regulation of oocyte mRNA as a partner of CPEB. However, Patl2's expression profile throughout oocyte development in mice, alongside colocalisation experiments with Cpeb1, Msy2 and Ddx6 (three oocyte RNA-regulators) suggest an original role for Patl2 in Mammals. Accordingly, transcriptomic analysis of oocytes from WT and Patl2-/- animals demonstrated that in the absence of Patl2, expression levels of a select number of highly relevant genes involved in oocyte maturation and early embryonic development are deregulated. In conclusion, PATL2 is a novel actor of mammalian oocyte maturation whose invalidation causes OMD in humans.

  Study EGAS00001002903

• High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors collected across Lymphoma/Leukemia Molecular Profiling Project sites. These tumors were profiled using whole-genome sequencing (WGS) or whole-exome sequencing (WES) to identify somatic mutations, WGS or low-pass WGS to detect copy number alterations, targeted capture sequencing to assess MYC and BCL2 structural variants, and RNA sequencing. The genetic features of HGBCL-NOS were compared to those of diffuse large B-cell lymphoma (DLBCL-NOS) and EBV-negative adult Burkitt lymphoma (BL). DLBCL-NOS tumors underwent targeted capture sequencing using a panel of 125 genes recurrently mutated in aggressive B-cell lymphomas. BL biopsies were drawn from the Burkitt Lymphoma Genome Sequencing Project and had available WGS (dbGaP Study Accession: phs000527.v18.p6).

  Study EGAS50000000932

• Genetic drivers of epigenetic and transcriptional variation of human immune responses to infection (RNA-seq, ATAC-seq and ChIPmentation)

  RNA-seq, ATAC-seq and ChIPmentation data from monocyte-derived macrophages that were infected with Influenza A virus strain PR8WT, or a matching non-infected control.

  Dataset EGAD00001008422

• Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer

  Mechanisms of acquired resistance to immune checkpoint inhibitors (ICIs) are poorly understood. The purpose of this study was to investigate whether alterations in genes encoding components of the HLA Class I antigen processing and presentation machinery or interferon signaling pathways play a role in acquired resistance to PD-1 or PD-L1 antagonistic antibodies. Whole exome sequencing was performed on tumor samples collected from patients with advanced non-small cell lung cancer at the time of resistance to PD-1 axis inhibitors and on available matched pre-treatment and normal samples. Patient-derived xenografts successfully established from the ICI-resistant samples were also exome sequenced. Additionally, RNA sequencing was performed on cases with sufficient tissue.

  Study phs001464

• Single-cell ATAC-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell ATAC sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015719

• Single-cell ATAC-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell ATAC sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015711

• Single-cell ATAC-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell ATAC sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015715

• RNAseq of whole blood in 359 idiopathic pulmonary arterial hypertension patients reveals biological heterogeneity

  Patients with idiopathic, heritable, or drug-induced pulmonary arterial hypertension (referred to throughout as PAH) were recruited from expert centers across the UK as part of the PAH Cohort study (www.ipahcohort.com). In each case, diagnosis was confirmed by right heart catheterization following established international guidelines, which remained unchanged for the duration of this study. Healthy volunteers were recruited at the same centers and samples processed using the same standard operating procedure at all sites. All individuals gave written, informed consent with local ethical committee approval. Whole blood (3 ml) was collected in Tempus Blood RNA Tubes, and RNAseq was performed using established Illumina methodologies (see online supplement for further details).

  Dataset EGAD00001007981

• Next Generation Sequencing of Stage IV Squamous Cell Lung Cancers Reveals an Association of PI3K Aberrations and Evidence of Clonal Heterogeneity in Patients with Brain Metastases

  Putative oncogenic pathways in squamous cell lung cancer have been recently characterized, although their biologic repercussions in patients is largely unknown. This study sought to discover potential clinical manifestations of major pathways in squamous cell lung cancer, particularly the PI3K pathway. Two key findings emerged: patients with stage IV squamous cell lung cancer whose tumors harbored upstream PI3K aberrations had significantly worse survival and a higher burden of metastatic disease. In addition, brain metastases were significantly more common in these patients than in others. Paired lung primary/brain metastasis genotyping, including RNA sequencing and whole exome sequencing, uncovered a high degree of genetic heterogeneity between lung/brain pairs, and identified potential regulators of the metastatic process to brain.

  Study phs000907

• Genomic Studies of Bipolar Disorder in a Large Cohort from The Netherlands

  The transcriptomes of whole blood samples of a large cohort of individuals from the Netherlands were assayed using RNA-seq. These whole blood samples included patients diagnosed with schizophrenia or bipolar disorder, family members of patients, and healthy controls. Within the whole blood dataset, about 600 of the samples were sequenced to an average of 13.9 million mapped reads per sample, while about 2,000 were sequenced to an average of 5.9 million mapped reads per sample, in order to assess changes in power to detect eQTLs based on sample size. We find that expression, defined as the log transcripts per million reads (TPMs), is highly correlated when comparing the moderate (13.9M) and lower (5.9M) coverage datasets. Additionally, a subset of about 150 individuals provided fibroblast cell lines which were assessed for the levels of gene expression using RNA-seq at an average of 50 million mapped reads per sample. We use downsampling techniques to generate synthetic datasets derived from this real fibroblast RNA-Seq data to explore the relationship between coverage and number individuals in an eQTL analysis. Corresponding individual-level genotypes for the samples included in the expression matrix are also made available. The genotypes were derived from multiple other project cohorts, each using different genotyping platforms including OmniExpress Exome, Global Screening Array, Illumina550, and PsychChip. A Plink file set of these cohorts is provided here after merging the separate project file sets and extracting only the individuals who have expression data also provided here; quality control for SNP-missingness is recommended. We demonstrate in this study that given a fixed budget, eQTL discovery power can be increased by lowering the sequencing depth per sample to allow for an a greater number of individuals sequenced. 

  Study phs002856