10161 results for "cancer rna-seq"

in 42.59 milliseconds.

• Epigenomic timecourse of brain organoid development

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. At each time point used scCut&Tag to profile histone modifications (H3K27me3, H3K27ac, H3K4me3) as well as multiome-seq (10X) to jointly profile transcriptome and chromatin accessibility from the same cell suspension. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000222

• FASTQ Data from In Situ Hi-C on Medulloblastoma Tissue Samples

  29 Hi-C datasets [8 G3 (MB3667, MB3687, MB3690, MB3692, MB3693, MB4010, MB4037, MB4141), 13 G4 (MB0558, MB3510, MB3670, MB3689, MB3716, MB3760, MB3761, MB3807, MB4079, MB4132, MB4174, MBSF7, SNC_2_5), 7 SHH (MB3612, MB3661, MB3662, MB3695, MB3697, MB3724, MB4143), and 1 WNT (MB4036)]. Fresh tissue samples were obtained from The Hospital for Sick Children (Toronto, ON). In situ Hi-C libraries were generated using approximately 2.5 million dissociated cells as input. All Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).

  Dataset EGAD50000000771

• CML_blast_phase_rearrangement_screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 10 Chronic Myeloid Leukemia in blast phase samples and subjected to a total of two lanes of 50 bp, paired end sequencing on the llumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions

  Study EGAS00001000191

• Myelodysplastic_Syndrome_Follow_Up_Series

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from MDS and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to discover the prevalence of our findings using bespoke pulldown methods and sequencing the products from a larger set of patient DNA.

  Study EGAS00001000224

• Genetic subclone heterogeneity of tumor-initiating cells in human colorectal cancer

  A subset of tumor-initiating cells (TIC) drives colorectal cancer (CRC) progression in serial mouse xenografts. The TIC compartment itself is heterogeneous and comprises hierarchically organized long-term TIC, tumor transient amplifying cells, and delayed contributing TIC. To address the genomic heterogeneity of the CRC TIC compartment, genome-wide high-coverage whole genome sequencing was performed on patient tumors (n=3), corresponding serially passaged TIC-enriched spheres, and serial xenografts.HIPO P002

  Study EGAS00001001857

• MutWP5__CRUK_Mutographs_of_Cancer__Breast__BRCA_Carriers__Targeted_

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer.

  Study EGAS00001003315

• MutWP5__CRUK_Mutographs_of_Cancer__Breast__BRCA_Carriers__Exome_

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer.

  Study EGAS00001003316

• MutWP5__CRUK_Mutographs_of_Cancer__Breast__Cancer_Mastectomy__Targeted_

  Sequencing of LCM-derived microbiopsies from 30 women who mastectomies due to Breast Cancer. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations.

  Study EGAS00001003318

• 1__Fanconi_Anemia_transformation_to_AML

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 7 Fanconi anemia (FA) derived Acute myeloid leukemia samples and subjected to total of two lanes of 50 bp, paired end sequencing on the llumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000033

• WGS and WES of 78 pairs Chinese gastric cancer

  Gastric Cancer (GC) is a highly heterogeneous disease. To identify potential clinically actionable therapeutic targets that may inform individualized treatment strategies, we performed whole-exome sequencing on 78 GCs of differing histologies and anatomic locations, as well as whole-genome sequencing on two GC cases, each with 3 primary tumours and 2 matching lymph node metastases. The data showed two distinct GC subtypes with either high-clonality (HiC) or low-clonality (LoC).

  Study EGAS00001001056

• Preservation of stemness in high-grade serous ovarian cancer organoids requires low Wnt environment

  High-grade serous ovarian cancer (HGSOC) likely originates from the fallopian tube (FT) epithelium, but advanced stages are mostly found outside the FT. We used ex-vivo cultures of HGSOC and knock-out of tumor suppressors in FT organoids to study changes in epithelial cells and niche requirements for normal and transformed FT cells. We found that transformed cells require BMP signaling and are growth arrested in Wnt rich medium.

  Study EGAS00001003821

• Circulating tumor cell copy-number heterogeneity in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

  Gatekeeper mutations are identified in only 50% of the cases at resistance to Anaplastic Lymphoma Kinase (ALK)-tyrosine kinase inhibitors (TKIs). Circulating tumor cells (CTCs) are relevant tools to identify additional resistance mechanisms and can be sequenced at the single-cell level. Here, we provide in-depth investigation of copy number alteration (CNA) heterogeneity in phenotypically characterized CTCs at resistance to ALK-TKIs in ALK-positive non-small cell lung cancer.

  Study EGAS00001005301

• Cholangiocarcinoma

  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 two datasets that contain NGS files from gastrointestinal rare cancers (n=119): - Dataset 2 (87 patients): Intra-hepatic cholangiocarcinoma (n=47), Extra-hepatic, cholangiocarcinoma (n=16), Not specified Cholangiocarcinoma (n=9), Small bowel adenocarcinoma (n=6) and other rare GI cancer (n=9)

  Dataset EGAD00001008968

• Sequencing of Cervical Cancer

  Precision mapping of genetic alterations in cancer can enable better selection of therapies and improved outcomes when combined with new sequencing diagnostics. We describe whole-exome sequences from cervical adenocarcinomas and paired normal samples in Hong Kong Chinese women. These data uncover a heterogeneous genomic landscape but identify commonly aberrant loci including FAT1, ARID1A, ERBB2 and PIK3CA that may provide a focus for the development of individualized targeted therapies for Chinese women with cervical adenocarcinoma.

  Study phs000723

• Multiregional Single-Cell Transcriptomic Analysis of Liver Cancer

  In this study, we performed single-cell transcriptomic profiling of human liver tissues collected from hepatocellular carcinoma and intrahepatic cholangiocarcinoma patients. A total of seven primary liver cancer patients enrolled in this study. Samples were collected from multiple regions, including tumor core, tumor border and adjacent non-tumor tissue. The 10x Genomics platform was used to generate single cell 5' libraries. The Illumina NovaSeq 6000 platform was employed for sequencing.

  Study phs003117

• Integrated Genomic and Transcriptomic Analysis of Small Cell Lung Cancer Reveals Inter- and Intratumoral Heterogeneity and a Novel Chemotherapy-Refractory Subtype

  We integrated histology, transcriptome, exome, and treatment outcomes of small cell neuroendocrine cancer (SCNC) from a range of metastatic sites, revealing complex intra- and intertumoral heterogeneity of neuroendocrine (NE) differentiation and transcriptomic subtypes (ASCL1, NEUROD1, POU2F3, YAP1 and ATOH1). High NE SCNCs were more likely to benefit from replication stress-targeted therapies, in contrast to non-NE tumors which were more likely to respond to immune response-targeted therapies.

  Study phs002541

• Platinum-based chemotherapy induces opposing effects on immunotherapy response-related spatial and stromal biomarkers in the bladder cancer microenvironment

  The goal of the current project was to investigate the modulation of the tumor-immune microenvironment (TME) by neo-adjuvant platinum-based chemotherapy in muscle-invasive bladder cancer. Furthermore, we aimed to focus on how this modulation affects biomarkers of response to immune checkpoint inhibitors. Additionally, we aimed to explore the differences between MVAC and gemcitabine-containing platinum-based regimens regarding their effects on the bladder TME.

  Study EGAS50000000309

• To_profile_the_landscape_of_sebaceous_tumours_WES

  Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract DNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted DNA will be used for exome sequencing.

  Study EGAS00001003553

• Shot-gun stool metagenomics and colorectal cancer risk.

  This study aims to identify metagenomics biomarkers in colorectal cancer (CRC). The study includes 156 samples of shot-gun stool metagenomics, corresponding to 51 patients with CRC, 54 patients with high-risk adenoma, and 51 healthy controls. The sequencing libraries were prepared with 2 µg of total DNA using the Nextera XT DN Sample Prep Kit (Illumina, San Diego, CA, USA). Sequencing was performed at 150 nucleotides, paired-end, using an Illumina HiSeq 4000 platform.

  Study EGAS00001007025

• Whole genome sequencing of pancreatic cystic fluid for early detection and diagnosis of pancreatic cancer

  Pancreatic cancer (PC) is a leading cause of cancer-related deaths globally. Accurate PC detection at early or premalignant stage, when surgery is effective, would increase survival rates and prevent unnecessary surgery or surveillance. Molecular diagnostic attempts using PCy fluid (PCyF), as a liquid biopsy, to analyze common mutations associated with PC development are yet to contribute to early diagnosis. Whole genome sequencing (WGS) is utilized in various cancers, PC inclusive, for detecting genetic changes associated with carcinogenesis, but not in PCyF due to technical limitations, including isolated DNA purity. The goal of the study was to achieve high quality of WGS from PCyF from 9 patients to enable development of signatures of malignancy. The WGS was performed using Illumina sequencing. Experimental design was at a 50x depth.

  Dataset EGAD50000000869

• Leeds_Melanoma_Cohort

  Leeds Melanoma Cohort

  Study EGAS00001001158

• Recurrent Somatic Mutations in CLL

  Study EGAS00001000070

• Human primary and metastatic colorectal cancer (CRC) samples

  Dac EGAC00001002954

• Genetic alterations in metastatic uveal melanoma

  Study EGAS00001003303

• OSCC WES + WGS Boot et al. 2020

  Study EGAS00001004376

• Ovarian Cancer Laboratory, University of Oxford

  Dac EGAC00001000518

• Lung Cancer Single-cell Data Access Committee

  Dac EGAC00001001220

• Breast Cancer Cell Line Data Access Committee

  Dac EGAC00001000134

• DAC for the Prostate Cancer Lymph Node dataset

  Dac EGAC00001000586

• The Ovarian Cancer Association Consortium Data Access Committee

  Dac EGAC00001000616

• Spatial Maps of Prostate Cancer Transcriptomes Data Access

  Dac EGAC00001000913

• Data Access Commitee for gastric cancer ascites

  Dac EGAC00001001026

• DAC for MCO colorectal cancer genomics at UNSW

  Dac EGAC00001001122

• DAC for GAMuT Project - Peter MacCallum Cancer Centre

  Dac EGAC00001001154

• DAC for GAMuT Project - Peter MacCallum Cancer Centre

  Dac EGAC00001001278

• DAC for Angiosarcoma Study. National Cancer Centre Singapore.

  Dac EGAC00001001311

• Hyperpolarized 13C MRI in breast cancer DAC

  Dac EGAC00001001438

• Metastases of a cancer of unknown primary (CUP)

  Dac EGAC00001001484

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001001500

• Hereditary Cancer Diagnostics with I2HCP Data Access Comitee

  Dac EGAC00001001541

• Inherited Predisposition to Cancer Projects Data Access Committee

  Dac EGAC00001001565

• Immunogenomics of Colorectal Cancer Data Access Committee

  Dac EGAC00001001596

• UZ Ghent Prostate Cancer Team Data Access Committee

  Dac EGAC00001001608

• Primary tumor and metastatic breast cancer data access

  Dac EGAC00001001687

• Cancer Alliance Data Access Committee

  Dac EGAC00001001641

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001001906

• Singapore Gastric Cancer Consortium Data Access Committee

  Dac EGAC00001001955

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001001988

• MSKCC Colorectal Cancer Plasma WGS Data Access Comittee

  Dac EGAC00001002741

• RNAseq analysis on metastatic Colorectal Cancer xenografts samples

  Dac EGAC00001002809