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• scRNAseq - Notch Signaling Maintains a Progenitor-Like Subclass of Hepatocellular Carcinoma

  To clarify the cellular composition and the mechanism of efficacy following JAG1/NOTCH2 inhibition, we performed single-cell sequencing of LIV78 tumors isolated from control animals or following inhibition of JAG1 or NOTCH2. The results suggest that sensitive tumors consist of heterogeneous populations of cells in distinct transcriptional states and that Notch signals emerge from ligand-receptor co-expressing cells.

  Study EGAS50000000517

• Data access to Small RNA-Seq of MicroRNA's in Tear EV's of Ushers Syndrome patients

  Via this DAC you can get access to Small RNA-Seq dataset of MicroRNA's in Tear EV's of Ushers Syndrome patients. The study involved genetically confirmed USH1B patients and their healthy relatives, with additional fibroblast samples from Spanish collaborators, to ensure a robust comparison of small non-coding RNAs (sncRNAs). Tear and blood samples were collected using non-invasive methods, and extracellular vesicles (EVs) were isolated from both tears and hiPSC-derived retinal pigment epithelium (RPE) cells. RNA was extracted from these EVs and assessed for quality before preparing libraries using the TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating data for comparative analysis of sncRNA profiles between patients and controls.

  Dac EGAC50000000711

• Transcriptomic profiling of T cells following ABHD11 inhibition

  This dataset contains paired-end RNA sequencing data from human T cells treated with ML226, a selective ABHD11 inhibitor, and matched vehicle controls. The experiment was designed to investigate the role of ABHD11 in sterol metabolism and its impact on T cell effector function and autoimmunity. Samples were collected across biological replicates following 24-hour treatment, and RNA was extracted for high-throughput sequencing. Sequencing was performed using an Illumina platform. The dataset supports analysis of differentially expressed genes, alternative transcript usage, and pathway-level effects of ABHD11 inhibition. This dataset is part of the study titled "ABHD11 inhibition drives sterol metabolism to modulate T cell effector function and alleviate autoimmunity".

  Dataset EGAD50000001845

• Differential expression in clear cell renal cell carcinoma

  To investigate the levels of gene expression in clear cell renal cell carcinoma (ccRCC), we performed an RNA-seq analysis in 786-O, A-498, UM-RC-2 clear cell renal carcinoma cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq files and csv files with the differential expression results. Differential expression was calculated by the RNAflow pipeline (DEseq2), and log fold changes are calculated with respect to the normal cell line (HK-2), with separate results between normoxic and hypoxic datasets.

  Dataset EGAD50000001883

• SCANDARE HNSCC 3' Tag RNA-seq

  SCANDARE (NCT03017573) is a multicentric biobanking study, enrolling adult patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC), triple negative breast cancer (TNBC), ovarian and cervical cancer. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Since its launch in 2017 at Institut Curie, SCANDARE has enabled the longitudinal collection and preservation of samples for in-depth analyses. Here, we describe molecular alterations in 264 FFPE samples at baseline from 90 HNSCC patients using 3'-tag RNA-seq technology, with FASTQ files deposited in the dataset.

  Dataset EGAD50000001655

• SCANDARE TNBC WES data

  SCANDARE (NCT03017573) is a multicentric biobanking study, enrolling adult patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC), triple negative breast cancer (TNBC), ovarian and cervical cancer. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Since its launch in 2017 at Institut Curie, SCANDARE has enabled the longitudinal collection and preservation of samples for in-depth analyses. Here, we describe molecular alterations in 247 frozen samples at baseline and 138 germline DNA from 139 TNBC patients using WES technology, with FASTQ files deposited in the dataset.

  Dataset EGAD50000001661

• SCANDARE TNBC WGS data

  SCANDARE (NCT03017573) is a multicentric biobanking study, enrolling adult patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC), triple negative breast cancer (TNBC), ovarian and cervical cancer. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Since its launch in 2017 at Institut Curie, SCANDARE has enabled the longitudinal collection and preservation of samples for in-depth analyses. Here, we describe molecular alterations in 108 FFPE samples at baseline and 108 germline DNA from 108 TNBC patients using WGS technology, with FASTQ files deposited in the dataset.

  Dataset EGAD50000001662

• Summarized somatic variant calls from CMMRD-associated high-grade gliomas

  This dataset contains summarized somatic variant call data derived from paired tumor–blood whole-exome sequencing of human samples. Access to the dataset is controlled and granted only upon submission and approval of a formal data access request. Requests are reviewed by the Data Access Committee led by the Principal Investigator to ensure compliance with applicable legal, ethical, and data protection requirements. Users must not attempt to re-identify study participants and must comply with all relevant confidentiality and data protection regulations. In accordance with local legal and ethical requirements, individual-level raw sequencing data are not shared.

  Dataset EGAD50000002180

• scMethylation data of 5 regionally sampled GBM tissue for 2 patients

  This dataset contains snRNA-seq data of 5 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed in an unbiased manner without any sorting procedure. Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. mplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.

  Dataset EGAD50000001837

• SCANDARE TNBC shallow WGS data

  SCANDARE (NCT03017573) is a multicentric biobanking study, enrolling adult patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC), triple negative breast cancer (TNBC), ovarian and cervical cancer. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Since its launch in 2017 at Institut Curie, SCANDARE has enabled the longitudinal collection and preservation of samples for in-depth analyses. Here, we describe molecular alterations in 251 frozen samples at baseline from 143 TNBC patients using shallow WGS technology, with FASTQ files deposited in the dataset.

  Dataset EGAD50000001849