12215 results for "cancer rna-seq"

in 22.13 milliseconds.

• Alternative splicing isoforms in patient-derived hepatocellular carcinoma cells

  The aim of this study was to obtain a landscape of alternative splicing (AS) in human hepatocellular carcinoma (HCC). We applied hybrid sequencing by integrating Pacbio long-read and Illumina short-read RNA sequencing data from 8 patient-derived HCC cell lines, and used an immortalized hepatocyte cell line as reference. This study revealed features of annotated and novel splice variants in HCC cells, including transcript length, AS type and protein changes. We also identified novel isoforms and tumor specific isoforms, which may represent potential biomarkers and targets for therapeutic development.

  Study EGAS00001002697

• ImmunoAgeing_Longitudinal

  The objective is to establish whether immunosenescence is associated with the development of clonal haematopoiesis in a healthy ageing population. This will be addressed in collaboration with the European consortium running the ImmunoAgeing project (www.immunoageing.eu). Genomic DNA derived from the peripheral blood of 394 individuals at 3-5 time-points over a 20-year period will be analysed. RNA bait pulldown (Agilent) will be used to perform targeted sequencing of genes known to be recurrently mutated in myeloid malignancies The presence, size and nature of clonal haematopoiesis will be correlated with quantitative measures of immunosenescence.

  Study EGAS00001003183

• Gene expression profiling of nasopharyngeal carcinoma

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Study EGAS00001004542

• An epigenetic single-cell atlas of IDH-mutant glioma reveals the role of ATRX in shaping tumor composition

  Recent single-cell RNA-sequencing studies have identified a hierarchy of cell types that is common to all isocitrate dehydrogenase (IDH) -mutant gliomas. This finding is somewhat paradoxical since the genetic differences between IDH-mutant astrocytomas and IDH-mutant oligodendrogliomas are prognostic, predictive of therapeutic response, and correlated with differences in immune infiltrates. To integrate these disparate findings, we constructed a single-cell atlas of 22 human IDH-mutant primary untreated grade-II/III gliomas.

  Study EGAS00001004523

• RNAseq data from human colon organoid infected by KP

  The aim of this study is to identify the specific bacteria that are responsible for pathological bacterial translocation and subsequent Th17 priming in the liver in primary sclerosing cholangitis (PSC). To clarify the mechanism of how microbiota interacts with the intestinal epithelial barrier, monolayered human intestinal organoids were cultured with the specific bacteria. Gene expression analysis using RNA sequencing in epithelial cells cultured with Klebsiella pneumoniae derived from a PSC patient (KP-P1) or commercially obtained Klebsiella pneumoniae strain (KP JCM1662) was performed in this study.

  Study EGAS00001003332

• Diagnosis of multisystem inflammatory syndrome in children by a whole-blood transcriptional signature

  To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki Disease (KD), bacterial infections and viral infections. Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020-April 2021 were prospectively recruited. Whole blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C to those from children with KD, definite bacterial and viral infections. Data deposited here comprises samples from patients recruited into the DIAMONDS study.

  Study EGAS00001007409

• Elucidation of factors involved in the progression of diabetic kidney disease

  A new concept of diabetic kidney disease has been proposed as a more comprehensive disease concept for chronic kidney disease associated with diabetes.The factors and molecular mechanisms that determine the course of diabetic nephropathy, whether it is the classic diabetic nephropathy or the rapid decliner, are unknown.In order to develop effective diagnostic and therapeutic methods for individual cases and conditions of diabetic nephropathy patients, it is necessary to elucidate the molecular mechanisms.We performed single-cell RNA sequencing and analyzed the characteristics of 3 cases of rapid decline in diabetic kidney disease.

  Study JGAS000802

• Mapping genetic variants that underlie gene regulation in intestinal cell types to identify novel, validated, Crohn’s disease drug targets

  Biopsies from the terminal ileum and rectum of healthy individuals and terminal ileum and blood from Crohns disease patients are collected and processed single cells and processed for single-cell RNA-sequencing using 10X Genomics 3' v3 and v3.1 and Illumina sequencing. 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 EGAS00001003647

• Bulk 3' mRNA-Sequencing of human ASC-derived kidney tubuloids

  Bulk 3' mRNA-Seq raw files (FASTQ) from human kidney tubuloids derived from 4 separate donors in collagen-based dome culture and suspension culture. Samples were collected for sequencing on day 7 of passage 3, 4, and 5. Total = 24 samples.

  Dataset EGAD50000002335

• Saliva_Fulani_Database

  In total, 90 DNA samples were genotyped on the Illumina Infinium H3Africa Consortium array (designed for 2,271,503 SNPs; using BeadChip type: H3Africa_2019_20037295_B1). Genotyping was performed at the SNP&SEQ Technology Platform (NGI/SciLifeLab Genomics, Sweden). Saliva Fulani dataset includes individuals from the following populations: 30 individuals from Senegal_FulaniLinguere, 30 individuals from Mauritania_FulaniAssaba, and 30 individuals from Mali_FulaniInnerDelta.

  Dataset EGAD50000000653

• TOTHER3 dataset

  This dataset contains the FASTQ and BAM files for TOTHER3 study. Targeted DNA-Seq experiment were realized with 49 samples. Since this data was obtained with a panel of genes protected by Intellectual Property (IP), these files only contain information to validate the results published and, in consequence, sensible data had to be specifically removed.

  Dataset EGAD50000000562

• Highly complex single-cell mixture of 5 individuals of high cell number

  Mixture of 5 unrelated individuals sequenced by 10x as a scATAC-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile using the De-goulash pipeline. The separation file is submitted as the processed file. The bam are submitted as unprocessed files.

  Dataset EGAD50000000480

• Tam-seq of tumor samples for HGSOC copy-number signatures study

  This dataset contains targeted amplicon sequencing of DNA extracted from 300 samples of 142 patients (158 methanol-fixed relapse biopsies and 142 FFPE archival diagnostic tissues). Samples were sequenced on Illumina HiSeq 2500 and were aligned to human genome assembly GRCh37 (hg19)to produce 600 bam files (2 technical replicates per sample).

  Dataset EGAD00001004173

• McGill EMC Community projects Release 7 for cell line "SaOS-2"

  Complete reference epigenome (as defined by IHEC) of a SaOS-2 cell line with osteosarcoma.

  Dataset EGAD00001007678

• CBD-RAW-SC-ADT: 10X Single-Cell Features Barcode (CITE-seq)

  Raw Illumina sequencing data and CellRanger BAM output files. For further information regarding this dataset, please contact Stephen Sansom at contact@combat.ox.ac.uk.

  Dataset EGAD00001007962

• Leukemia stem cell containing fractions

  AML bulk samples were sorted into fractions based on expression of CD34 and CD38, LSC activity in each fraction was assessed by xenotransplantation into NOD. Prkdcscid. Il2rgnull(NSG) mice. ATAC-seq was used to profile the accessible chromatin landscape of 11 LSC+, 24 LSC- fractions . 50,000 cells from each sample were processed. Libraries were sequenced with 50bp single-end reads.

  Dataset EGAD00001006775

• Multiple Myeloma ChipSeq data on six histone modifications

  The data contained in this dataset is ChipSeq BAM files aligned to reference genome hg38. The ChipSeq was based on a combination of six histone modifications as follows: H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K27Ac and H3K36me3. The samples are patient-derived xenografts generated by passaging primary patient CD138+ selected cells through the SCID-rab myeloma mouse model.

  Dataset EGAD00001008353

• Mixture of 2 (closer mtDNA)

  Mixture of 2 unrelated individuals (of close mtDNA haplogroup) sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008727

• scRNA-seq of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10551

  Dataset EGAD00001009386

• dbGaP submission of CORECT OncoArray GWAS data

  This analysis represents the genome-wide association study results of several international case-control studies of colorectal cancer.

  Study phs001903

• Multi-omic profiling of patient-derived pancreatic tumor organoids

  We conducted multi-omic profiling of patient-derived pancreatic cancer organoids and genetically engineered normal pancreas organoids.

  Study JGAS000719

• checup

  Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial)

  Study EGAS00001007403

• WGBS dataset for lymphnode metastasis samples from prostate cancer

  This dataset contains WGBS sequencing data of lymphnode metastasis samples from prostate cancer. Sequencing was performed on Illumina HiSeq X Ten. The sequencing was always paired.

  Dataset EGAD50000001183

• INVADE bulk RNAseq

  Fastq files of bulk RNAseq data from DCIS, invasive and microinvasive breast cancer at diagnosis. This dataset covers 18 DCIS cases, 17 microinvasive and 20 primary invasive breast cancer.

  Dataset EGAD50000000320

• Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Dataset EGAD00001000293

• Paired-end sequenced plasma DNA samples

  Merged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments.

  Dataset EGAD00001002217

• Amplicon sequencing of adenoma to carcinoma paired samples from colon

  Colorectal cancer panel sequencing of 100 adenoma and carcinoma samples . Cancer Hot Spot panel sequencing of 7 samples from one poly.

  Dataset EGAD00001004848

• Ovarian cancer sequencing dataset

  Sequencing data from patients with Ovarian cancer. Data utilised in the 'Enhanced detection of circulating tumor DNA by fragment size analysis' manuscript (Mouliere et al, 2018)

  Dataset EGAD00001004939

• Epigenomic profile of diverse cancer

  The samples are from patients of multiple cancer types. The library preparation protocol was developed by the laboratory. The DNA libraries were then sequenced with 150bp paired-end reads.

  Dataset EGAD00001006124

• SPECTA Lung cancer DNA FASTQ files

  SPECTA Lung cancer DNA FASTQ files (Illumina TST170 targeted analysis)

  Dataset EGAD00001006223

• WES data of serially passaged TIC-enriched spheres of colorectal cancer

  WES data of serially passaged TIC-enriched spheres of colorectal cancer (CRC)

  Dataset EGAD00001006266

• Rapid identification of somatic genome rearrangements as personalized biomarkers for blood-based cancer monitoring

  Increasing evidence shows the value of circulating tumour DNA (ctDNA) to detect cancer and monitor its progression. Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of ctDNA in liquid biopsies. However, accurate, affordable, and fast identification of such SV biomarkers is challenging, which hinders routine use in the clinic. Here, we demonstrate a novel approach - termed SHARC - for rapid discovery of somatic SV breakpoints as personalized tumour biomarkers. SHARC combines low-coverage cancer genome sketching by using Oxford Nanopore portable sequencing with a random forest classification and a dedicated filtering pipeline to enrich for somatic SVs. Our method leverages the real-time and long-read capabilities of Nanopore sequencing to identify somatic SV breakpoints at nucleotide resolution from a tumour biopsy within two days. We applied SHARC to tumour samples of high-grade ovarian and prostate cancer and validated on average 10 somatic SVs per sample with the use of PCR mini-amplicons. Finally, we demonstrate that these somatic SV biomarkers can be used to detect tumour presence from liquid biopsies in a quantitative manner and we retrospectively monitored treatment response in patients with prostate cancer, demonstrating its potential benefit for clinical practice.

  Study EGAS00001003963

• Recurrent intra-tumour heterogeneity is a hallmark of metastatic prostate cancer

  The evolution of cancers from low grade to metastatic disease is a major determinant of cancer mortality. Cancer evolution involves a complex interplay between cell intrinsic genetics and transcriptional alterations and the extrinsic microenvironment. To define the key mechanisms underpinning metastatic development, we focused on the most lethal form of prostate cancer, metastatic castration-resistant prostate cancer, and employed single-cell multi-omics and whole-genome sequencing to deeply profile 34 metastatic lesions from 9 patients obtained from rapid autopsy. We found that intra-tumour heterogeneity is an indicator of key evolutionary processes, characterised by recurrent tumour populations acting as critical functional components of the tumour ecosystem, irrespective of clonal and microenvironmental backgrounds. Unexpectedly, microenvironments across metastatic sites played a limited role while clonal evolution primarily promoted transcriptional noise. Intra-patient functional convergence of tumour ecosystems was observed across metastatic sites, pointing towards system-level selection pressures that drive the heterogeneity landscape of mCRPC. Our findings reveal functional evolutionary convergence of metastatic disease into units of intra-tumour heterogeneity identifying critical determinants of metastatic progression for therapeutic targeting. Note: matched WGS for some tumour single-cell experiments, as well as germline WGS for patients CA0027, CA0034, CA0035, CA0043, and CA0076, can be found in EGAS00001006598.

  Study EGAS50000001312

• Genomic Alterations in Gingivo-buccal Cancer: ICGC-India Project_YR02

  As a part of the ICGC, India has undertaken genomic studies on gingivobuccal cancer of the oral cavity, which is the most prevalent form of cancer among men in India. There are various known environmental (life-style) correlates of this cancer, the most important of which are tobacco chewing and HPV infection. Paired DNA samples – isolated from the tumour tissue and from the blood of fifty six patients – have been analyzed to catalog germline and somatic mutations. Association between each observed genomic alteration and exposure to environmental risk factors is being explored.Detailed clinical characterization of the patients, collection of data on demographic and environmental exposures, and isolation of DNA samples from blood and tumour tissues collected from each patient are being done at the Advanced Centre for Research, Treatment and Education on Cancer, Mumbai. Exome capture and deep resequencing are being performed at the National Institute of Biomedical Genomics, Kalyani. We have analyzed the exomes of paired blood and tumour DNA samples using exome capture by Illumina TrueSeq Exome Enrichment kit followed by sequencing on Illumina HiSeq-2000. Each exome is being sequenced at a mean depth of 70x for Tumour and 40x for Blood. In addition, we have used Illumina Omni 2.5 SNP-chips to generate genotype data.

  Study EGAS00001001028

• Quantitative analysis of a novel DNA hypermethylation panel for lung cancer diagnosis using bronchial specimens

  Non-diagnostic findings in Transbronchial Lung Biopsy (TBLB) and Endobronchial Ultrasound-guided Transbronchial Lung Biopsy (EBUS-TBLB) are not uncommon. A challenge is to improve lung cancer detection by TBLB/EBUS-TBLB. In order to improve the diagnostic yield of bronchoscopy, we used 850K methylation chip to identify methylation sites that distinguish malignant from benign lung nodules.We found that the combination of HOXA7, SHOX2,and SCT methylation analysis has the best diagnostic yield in 123 bronchial washing (sensitivity: 74·1%; AUC: 0·851) and 172 brushing samples (sensitivity: 86·1%; AUC: 0·915). We developed a kit comprising these three genes and validated the kit in 329 unique bronchial washing samples, 397 unique brushing samples, and 179 unique patients with both washing and brushing samples. The diagnostic accuracy of the panel alone in lung cancer diagnosis was 86·9%, 91·2% and 95% in bronchial washing, brushing, and washing+brushing samples, respectively. The panel's sensitivity in combination with cytology, rapid on-site evaluation (ROSE), and histology in lung cancer diagnosis was 90·8% and 95.8% in bronchial washing and brushing samples, respectively, and 100% in washing+brushing samples. Quantitative analysis of the three-gene panel improves lung cancer diagnosis by bronchoscopy.

  Study EGAS00001007089

• Mutational Landscape of MCPyV-Positive and MCPyV-Negative Merkel Cell Carcinomas

  Merkel cell carcinoma (MCC) is an aggressive neuroendocrine carcinoma of the skin most commonly found on the sun-exposed skin of older Caucasian adults. Roughly one-third of patients with MCCs die of the disease; therefore, MCC is the most lethal skin cancer on a case-by-case basis. 49 cases were studied, and putative cancer driver gene mutations and tumor antigens in both MCPyV-negative and MCPyV-positive MCCs were identified.

  Study phs002515

• Germline Sequencing for Aggressive Prostate Carcinoma

  This study aims to elucidate the genetic determinants of susceptibility to aggressive prostate carcinoma. To this end, germ line whole exome sequence has been generated from patients with aggressive prostate cancer. Whole genome sequence for a representative subset of tumors from patients whose cancer was resistant to primary therapy is included as well. This deep genomic interrogation will allow the identification of rare, functionally disruptive variants that may play a role in disease progession and response to treatment.

  Study phs000661

• Modelling Multi-Dimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research

  The Center for Cancer Research (CCR), of the intramural NCI undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers who were enrolled on other therapeutic trials to determine the feasibility of a genome guided precision therapy protocol in these patients.Note: NCIPM001blood - This sample was previously submitted with study phs002207, with sample ID NCIPM001blood_E and SRR ID SRR18544311.

  Study phs001052

• Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration

  The human papillomavirus (HPV) genome is integrated into host DNA in most HPV-positive cancers, but the consequences for chromosomal integrity are unknown. We used continuous long-read sequencing of oropharyngeal cancers and cervical cancer cell lines to resolve structural variation induced by HPV. We discovered a previously undescribed form of structural variation, "heterocateny," characterized by diverse, interrelated, and repetitive patterns of concatemerized virus and host DNA segments within a cancer.

  Study phs003396

• Circulating cell-free and extracellular vesicles-derived microRNA as prognostic biomarkers in patients with early-stage NSCLC: results from RESTING study

  Lung cancer, especially non-small cell lung cancer (NSCLC), has high mortality rates. Early-stage NSCLC shows a 50% relapse rate post-surgery, with most recurrences occurring within two years and a 5-year survival of only 30%. This study focuses on the prognostic value of circulating miRNAs in surgically treated ES-NSCLC patients, aiming to assess their predictive accuracy and compare them to standard prognostic factors.

  Study EGAS50000001032

• Genomic Signatures of Intestinal Metaplasia in Six Countries with Varying Incidence of Stomach Cancer

  Intestinal metaplasia (IM) is a pre-cancerous condition associated with gastric cancer (GC), a deadly malignancy with varying geographic incidence. Performing a genomic analysis of over 1,500 IM samples from six countries, we identified 46 significantly mutated genes. We observed IM driver genes associated with high-risk populations and worse prognosis (ARID1A), members of the KRAS/MAPK signalling pathway (KRAS, BRAF, MAP2K1, MAP3K1, MAP2K4, NF1), and altered mucosal immunity (PIGR).

  Study EGAS50000001056

• Copy-number signatures and mutational processes in ovarian carcinoma

  This study contains the data underlying our approach for copy-number signature identification in high-grade serous ovarian cancer. The samples studied are part of the BriTROC-1 consortium, a national study into relapsed high-grade serous ovarian cancer. The dataset consists of shallow-whole genome sequencing of 300 samples from 143 patients with match tagged-amplicon sequencing of TP53. The study also contains deeper whole-genome sequencing of 48 cases.

  Study EGAS00001002557

• Arcagen – thoracic malignancies

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files from rare thoracic malignancies (n=102)

  Study EGAS50000000123

• Panel sequencing of endocrine-resistant breast cancer

  Patients with endocrine-resistant breast cancer in Stockholm Sweden. DNA obtained from patients primary and relapse tumors, and tumor-free lymph nodes used as germline control. DNA was extracted from formalin-fixed paraffin-embedded tissue and sequenced by 370-gene panel-based sequencing with Kapa HyperPlus library preparation and Twist Bioscience hybrid capture. Custom bait sets (panels) from Twist Bioscience. Paired end 2x150 bp using NovaSeq X. The data is presented as fastq-files.

  Study EGAS50000000236

• Stratton__WGS___RCC___Japan

  The Stratton team uses DNA sequencing for somatic mutations to advance understanding of the causes of cancer. In particular, the investigation of “mutational signatures”, which report the mutational processes operative over the lifetime of each individual, to understand whether they are generated by endogenous or exogenous exposures and the extent to which these vary between human populations. Our work brings together global cancer epidemiology and genomics and is particularly characterised by large-scale multinational studies.

  Study EGAS00001008001

• Genomic study of an AT-AML

  Ataxia Telangiectasia (A-T) is caused by biallelic mutations in ATM and confers predisposition to cancer, with acute myeloid leukaemia (AML) being rarely observed. We investigated an AML arising in an A-T patient for secondary genetic events by performing whole exome sequencing of serial samples over the disease course. AML samples were compared to a reference "germline" sample from a much earlier time point. Goldgraben et al 2020, Pediatric Blood & Cancer

  Study EGAS00001004392

• WGS of peripheral blood leukocytes from patients with Li-Fraumeni syndrome

  We performed whole genome sequencing on 84 LFS family members from 47 families: 22 with wildtype TP53 and 62 with variant TP53. The variant TP53 cohort consists of 49 individuals who developed cancer and 13 individuals who remain cancer-free; 34 were from 13 families with 2-4 individuals sequenced within a given family and the remaining 28 had no family members sequenced. The wildtype cohort consists of 14 individuals who developed cancer and 8 individuals who are cancer-free, from 6 families.

  Dataset EGAD00001010200

• Longitudinal Multi-Omic Immune Resource Reveals Dynamic Responses in Healthy Human Aging

  The generation and maintenance of protective immunity is a dynamic interplay between host and environment that is impacted by age. Understanding fundamental changes in the healthy immune system that occur over a lifespan is critical in developing interventions for age-related susceptibility to infections and diseases. Here, we use multi-omic profiling (scRNA-seq, proteomics, flow cytometry) to examine human peripheral immunity in over 300 healthy adults, with 96 young and older adults followed over two years with yearly vaccination. The resulting resource includes scRNA-seq datasets of >16 million PBMCs, interrogating 71 immune cell subsets from our new Immune Health Atlas. This study allows unique insights into the composition and transcriptional state of immune cells at homeostasis, with vaccine perturbation, under Cytomegalovirus (CMV) infection and across age. We find that T cells specifically accumulate age-related transcriptional changes more than other immune cells, independent from inflammation and chronic perturbation. Moreover, impaired memory B cell responses to vaccination are linked to a Th2-like state shift in older adults' memory CD4 T cells, revealing possible mechanisms of immune dysregulation during healthy human aging. This extensive resource is provided with a suite of exploration tools at https://apps.allenimmunology.org/aifi/insights/dynamics-imm-health-age/ to enhance data accessibility and further the understanding of immune health across age. Please note that the Sound Life Cohort raw data are spread across three dbGap submissions: phs003841.v1 (this study), phs003944.v1, and phs003400.v1.

  Study phs003841

• scRNAseq data of CAP

  Fastq files from scRNAseq data of cancer associated pericytes-like from 3 patients. CAP were isolated from a total of 3 primary BC (surgical residues prior to any treatment) by using BDFACS ARIA III sorter (BD Biosciences). BC were collected directly from the operating room after surgical specimen macroscopic examination and selection of areas of interest by a pathologist. Samples were cut into small pieces (around 1 mm3) and digested in CO2-independent medium (Gibco #18045-054) supplemented with 150 μg/mL liberase (Roche #05401020001) and Dnase I (Roche #11284932001) for 40 min at 37°C with shaking (180 rpm). After digestion, cells were processed and stained as described above (#Flow Cytometry analysis of BC samples). CAP fibroblasts were then gated on the Live/Dead negative fraction and defined as EPCAM- CD45- CD31- CD235a- FAPMed CD29High. CAP scRNA-seq: Upon isolation, CAP cells were directly collected into RNase-free tubes (Thermo Fisher Scientific, #AM12450) precoated with DMEM (GE Life Sciences, #SH30243.01) supplemented with 10% FBS (Biosera, #1003/500). Single-cell capture, lysis, and cDNA library construction were performed using Chromium system from 10X Genomics, with the following kits: Chromium Single Cell 3′ Library & Gel Bead Kit v2 kit (10X Genomics, #120237) and Chromium Single Cell A Chip Kits (10X Genomics, #1000009). Generation of gel beads in Emulsion (GEM), barcoding, post GEM-reverse transcription cleanup and cDNA amplification were performed according to the manufacturer’s instructions. Cells were loaded accordingly on the Chromium Single cell A chips, and 12 cycles were performed for cDNA amplification. cDNA quality and quantity were checked on Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit (Agilent, #5067-4626) and library construction followed according to 10X Genomics protocol. Libraries were next run on the Illumina HiSeq (for patients P1) and NovaSeq (for patients P2–3) with a depth of sequencing of 50,000 reads per cell.

  Dataset EGAD50000000321

• Next-generation sequencing raw data from metastatic prostate cancer biopsies - observational study Vall d'Hebron Institute of Oncology (Ethics committee code PR-AG-5248)

  Paired tumor-normal whole exome sequencing data from patients with metastatic prostate cancer; dataset from Arce-Gallego et al, Cell Reports Med 2024

  Dac EGAC50000000448