FASTQ-files of EM-seq experiments of 6 primary human thymocyte subsets, isolated by flow-cytometry (FACS) from neonatal thymus biopsies. All samples were sorted to be negative for the expression of the lineage surface markers CD11c, CD19, CD56, CD141 and CD303 and additionally had the following surface phenotypes: DN2 (CD4-CD8-CD7+CD1a-CD161-CD38+CD3-TCRab-); DN3 (CD4-CD8-CD7+CD1a+); ISP (CD4+CD8-CD3-TCRab-CD1a+); DPE (CD4+CD8+TCRab-CD69-); DPL (CD4+CD8+TCRab+CD69+); SP4 (CD4+CD8-). Samples were sorted from 1-2 pediatric patients undergoing heart surgery.
Adult T-cell leukemia/lymphoma (ATL) develops via stepwise accumulation of gene mutations and chromosome aberrations. However, the molecular mechanisms underlying this tumorigenic process are poorly understood. We aim to elucidate the mechanism of the tumorigenic process involving genomic aberrations by CD30 signaling in HTLV-1���infected T-cells.
Between November 2010 and May 2014, 20 cases—17 thymomas and 3 thymic carcinomas (including 2 squamous and 1 neuroendocrine carcinoma)—were newly sequenced from surgically removed TETs at Seoul National University Hospital, with written informed consent. Tumors and normal tissues were carefully separated and immediately preserved in liquid nitrogen after resection. DNA and RNA were extracted from the tumors, adjacent normal tissues, and/or blood samples. Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit following standard Illumina protocols.
Between November 2010 and May 2014, 20 cases—17 thymomas and 3 thymic carcinomas (including 2 squamous and 1 neuroendocrine carcinoma)—were newly sequenced from surgically removed TETs at Seoul National University Hospital, with written informed consent. Tumors and normal tissues were carefully separated and immediately preserved in liquid nitrogen after resection. DNA and RNA were extracted from the tumors, adjacent normal tissues, and/or blood samples. Libraries for WES were prepared using the SureSelect XT (Human All Exon + UTR v5) Library Prep Kit following standard Illumina protocols.
This deposit consists of DNA and RNA sequencing data from 32 EPS patients. 28 samples had tumor DNA sequencing data. 2 had matched normal sequencing data. 27 samples had tumor RNA sequencing data.
Solve-RD data submitted to the ERN-GENTURIS cohort for re-analysis (Data freeze 1+2) v1
Clinical & biomarker data from IMagyn050: treatment arm, treatment approach, outcome of surgery, ECOG PS, PD-L1 status, race, age, disease stage, progression free survival (investigator assessed), overall survival, histology, tumor mutation burden and status, genomic loss of heterozygosity, microsatellite status, BRCA1/2 mutation status, tissue of origin. Mutation status based on FoundationOne NGS for the following genes is also being provided: TP53, BRCA1, CCNE1, MYC, NF1, PIK3CA, RAD21, TERC, PRKCI, KRAS, RB1, BRCA2, ARID1A, AKT2, PTEN, KDM5A, NOTCH3, FGF12, ERBB2, CDK12, EMSY, WHSC1L1, BCL2L1, CDKN2A, GNAS, ARFRP1, ZNF217, SOX2, CCND2, FGF6, FGF23, LYN, MUTYH, AURKA, FGFR1, MCL1, MLL2, MYCL1, ZNF703, BRAF, MAP2K4, CREBBP, TSC2
RNA-sequencing was carried out on ascetic fluid-isolated mesothelial cells from low-grade serous ovarian cancer patients, high-grade serous ovarian cancer patients, chemotherapy-treated high-grade serous ovarian cancer patients and control mesothelial cells obtained from non-oncologic patients to identify differentially expressed genes associated to mesothelial-to-mesenchymal transition process. The dataset contains 18 samples: - Control mesothelial cells: 4 samples - Group 1, high-grade serous ovarian cancer patients: 3 samples - Group 2, chemotherapy-treated high-grade serous ovarian cancer patients: 5 samples - Group 3, low-grade serous ovarian cancer patients: 6 samples
WES using IDT xGen Research Exome on Illumina NovaSeq 2x150bp: Normal sample (buffy coat), cecum tumor biopsy at diagnosis, ileocecal valve region tumor sample at week 19, pericolonic metastasis at week 19, lymph node metastasis at week 19, peritoneal metastasis at week 19. Week 19 samples from hemicolectomy. Deep coverage cfDNA NGS using PanCeq pan-cancer panel on NextSeq 2x150bp: week 2 and week 10.
Tumor transcriptome and whole exome sequencing data (matched tumor/normal for somatic mutation calling) along with key phenotypic information are provided for patients enrolled in the phase 2 IMmotion150 trial, assessing efficacy of atezolizumab monotherapy or combination of atezolizumab and bevacizumab versus standard of care (sunitinib) in 1L renal cell carcinoma. This data set accompanies the respective Nature Medicine publication (PMID: 29867230).
