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• Dataset for melanoma-RNA

  Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008858

• Dataset for hematopoietic_malignancy-RNA

  Rare cancer sequencing data of 47 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008860

• Dataset for gynecologic_cancer-RNA

  Rare cancer sequencing data of 48 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008856

• scRNA-seq and snRNA-seq of trophoblast stem cells (TSCs) differentiation into extravillous trophoblast organoids (EVTs)

  This dataset is part of a study that aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. This specific dataset includes scRNA-seq and snRNA-seq data from trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) together with EVT differentiation media. This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells. Data for primary trophoblast organoids is available under E-MTAB-12650.

  Dataset EGAD00001010017

• UCSF-CASCADE analysis of metastatic prostate cancer

  Targeted cancer therapy inevitably selects for tumor cells that harbor some form of therapy resistance. This phenomenon is a principle reason why advanced prostate cancer, which can be treated with agents targeting androgen signaling dependency and DNA repair failure, is a lethal condition. The influence of a patient's clinical history and disease evolution on how their disseminated tumors develop resistance has been difficulty to study, because few autopsy studies have been performed in heavily treated patients with DNA-repair deficient metastatic castration-resistant prostate cancer (mCRPC). Here, we assessed how resistance to targeted cancer therapies evolved in an autopsy cohort of 54 mCRPC tumors from six men. This dataset includes targeted sequencing, exome sequencing, and RNA-seq conducted on these biopsies.

  Dataset EGAD00001010275

• An integrated single-cell reference atlas of the human endometrium

  This dataset includes both the anchor scRNA-seq and snRNA-seq datasets used to build the Human Endometrial Cell Atlas (HECA). HECA provides a comprehensive definition of endometrial cell types and states throughout the menstrual cycle in donor with and without endometriosis. It identifies consensus cell types across datasets generated by teams worldwide, as well as previously unreported cell types, all of which are validated and mapped in situ using spatial transcriptomics. Processed data is available from ArrayExpress with accession number E-MTAB-14039. See Marečková, M., Garcia-Alonso, L., Moullet, M. et al. An integrated single-cell reference atlas of the human endometrium. Nat Genet 56, 1925–1937 (2024) https://doi.org/10.1038/s41588-024-01873-w for more information.

  Dataset EGAD00001015446

• NLG-LBC-05 ctDNA project sequencing data

  Low-pass whole-genome sequencing of pretherapy lymphoma cfDNA and targeted sequencing of cfDNA, tumor tissue and whole-blood samples of NLG-LBC-05 patient samples and cfDNA of nine subjects with no known cancer. Hybrid capture target enrichment; panel target and sequencing information provided in PMID:34932792. FASTQ files provided for targeted sequencing, separate sequencing runs per sample noted with prefix "run" if applicable. Sequences from DTX1 and KLHL6 targets are advised to be excluded from analyses due to PCR/plasmid contaminants of in-house origin.

  Dataset EGAD00001009337

• 5 scRNA-seq with TCR Enrichment of Tumour-Involved Lymph Nodes, Malignant Seromas and Patient-Derived Xenografts from 18 T-Cell Lymphoma Patients

  This raw data contains 5' scRNA-seq with TCR enrichment data from 18 individual patients analysing cells taken from tumour-involved lymph nodes (LN), malignant seromas and patient-derived xenografts (PDX) including systemic/nodal ALK+ ALCL (n=3 PDX), BIA-ALCL (n=2 seromas), PTCL-NOS (n=5 nodal tumours), nodal T follicular helper lymphoma - angioimmunoblastic type (nTFHL-AI) (n=1), nTFHL, not otherwise specified (nTFHL, NOS, n=1), TLBL (n=5) and 1 case of Sezary Syndrome (SS, cutaneous tumour). Droplet-based 5’ scRNA-seq with TCR enrichment (10x Chromium platform) was performed for all live cells, or the viable CD45+CD3- and CD45+CD3+ fractions following cell sorting by flow cytometry.

  Dataset EGAD00001015703

• sWGS of OV04 patient samples for ACN rascal study

  This dataset contains 142 .bam files of shallow WGS data (~0.1X) from OV04 patient samples. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008121

• Longitudinal study of whole blood gene expression in Kenyan children exposed to malaria

  We have collected RNA samples from whole blood of Kenyan children exposed to malaria in the Kilifi region of Kenya. Collections were performed each year from 2015 until 2018. This is a follow-up study to that described in Bediako et al. (in preparation). The SIMS consortium is seeking to identifying the underlying reasons why some children are more susceptible to malaria than others. In this study we hope to track changes in children’s immune systems over time which relate to the number of malaria episodes they experience. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001015405