EXPERIMENT_TITLE: Arima HiC Library preparation and Illumina 2x150 Sequencing of the GIAB HG008-T tumor cell line (Pancreatic Ductal Adenocarcinoma)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The Genome in a Bottle Consortium (www.genomeinabottle.org) is a collaboration between NIST, FDA, NCBI, other government agencies, academic sequencing groups, sequencing technology developers, and clinical laboratories. A principal motivation for this consortium is to develop widely accepted reference materials and accompanying performance metrics to provide a strong scientific foundation for the development of regulations and professional standards for clinical sequencing. NIST is developing large batches of human genome DNA from several cell lines for NIST Reference Materials (RMs), which will be characterized by the Consortium for homogeneity, stability, and sequence with as much sequencing technologies and library preparation methods as possible. Information from these datasets will be integrated to form a high-confidence set of genotype calls, which can be used by clinical and research laboratories to understand performance of their sequencing and bioinformatics methods. NCBI is serving as the DCC and repository for the raw sequencing reads, mapped reads, genotypes, and other details for each sample on a dedicated FTP site ( ftp://ftp-trace.ncbi.nih.gov/giab/ftp/ ). The pilot sample is NA12878 (HG001), and NIST received over 8,000 aliquots in April 2013, which will initially be distributed to partners in the Consortium to assist in characterization, and later will be distributed by NIST as Reference Material 8398, likely in March or April 2015. Samples from an Ashkenazim trio (son HG002-NA24385-huAA53E0, father HG003-NA24149-hu6E4515, and mother HG004-NA24143-hu8E87A9), and a Han Chinese trio (son HG005-NA24631-hu91BD69, father NA24694-huCA017E, and mother NA24695-hu38168C) from Personal Genome Project (PGP) are also candidate NIST reference materials and are currently being characterized. The Ashkenazim trio will be available both as NIST RMs 8391 (son only) and 8392 (entire trio). Only the son of the Asian trio will be a NIST RM (8393). DNA and cell lines for all samples are also available from Coriell, but the NIST RMs are from a single homogenized batch of DNA, so there may be small differences between the samples at Coriell and the NIST RMs. Details about the NIST Reference Materials, data, and future plans are at https://sites.stanford.edu/abms/content/giab-reference-materials-and-data. When the NIST RMs are available, they can be purchased from NIST at http://www.nist.gov/srm/, where a Report of Investigation describing the DNA will also be available.
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "GIAB HG008"}, {"TAG": "age", "VALUE": "61"}, {"TAG": "biomaterial_provider", "VALUE": "Massachusetts General Hospital (MGH)"}, {"TAG": "collection_date", "VALUE": "2020-12-30"}, {"TAG": "geo_loc_name", "VALUE": "USA"}, {"TAG": "sex", "VALUE": "female"}, {"TAG": "tissue", "VALUE": "Pancreatic Ductal Adenocarcinoma Cell Line (PDAC)"}, {"TAG": "disease", "VALUE": "pancreatic ductal adenocarcinoma"}, {"TAG": "sample_type", "VALUE": "cell culture"}, {"TAG": "super_population_code", "VALUE": "EUR"}, {"TAG": "super_population_description", "VALUE": "European"}, {"TAG": "is_tumor", "VALUE": "yes"}, {"TAG": "isolation_source", "VALUE": "pancreatic ductal adenocarcinoma"}, {"TAG": "cell_line", "VALUE": "HG008-T"}, {"TAG": "cell_subtype", "VALUE": "epithelial-like"}, {"TAG": "cell_type", "VALUE": "pancreatic ductal adenocarcinoma"}, {"TAG": "disease_stage", "VALUE": "tumor stage ypT2 N1, histological grade G2 (Moderately differentiated)"}, {"TAG": "treatment", "VALUE": "neoadjuvant therapy, tumor regression grade 2 (Minimal response: Residual cancer outgrown by fibrosis)"}, {"TAG": "passage_history", "VALUE": "The individual (HG008) was explicitly consented for tissue collection and public genomic data sharing following a Massachusetts General Hospital (MGH) IRB-approved protocol. The Liss laboratory at MGH established a PDAC tumor cell line (HG008-T) from the resected PDAC tumor. PDAC tumors are stromal-rich, with cancer cells often only composing 10% of the tumor. The cell line was developed starting with approximately 50 mg of tumor tissue being enzymatically dissociated to culture tumor cells. While PDAC cell cultures often contain substantial fibroblasts, all cells appeared to be tumor cells even at passage 2 for this cell line. Cells were cultured for the first 20 passages using \"Rich\" media composed of DMEM/F12 with 20% Fetal Bovine Serum (FBS) Nicotinamide (0.01 M), cholera toxin (8.4 ng/ml), Epidermal Growth Factor (EGF; 10 ng/ml)., Hepatocyte Growth Factor (HGF: 25 ng/ml), human recombinant insulin (10 ug/ml), human recombinant transferrin (5.5 ug/ml), and selenious acid (6.7 ng/ml). Morphologically pure cancer cell cultures, free of tumor-associated fibroblasts, were considered cell lines after growing for at least 20 passages. Passages 21-24 were grown the same media as prior passages however without EGF. A large homogenous batch (batch 0823p23) of tumor cells was cultured and at passage 23, approximately 80 million tumor cells were aliquoted, pelleted and snap-frozen for distribution and measurement of non-viable cells."}, {"TAG": "passage_method", "VALUE": "Cells were enzymatically removed from the culture surface using 0.25% trypsin and split by diluting no more than 1:3 for the first 20 passages. Passages 21-24 were diluted 1:3."}, {"TAG": "passage_number", "VALUE": "Liss_0823p23"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "HG008-T_HiC-Arima_ILMN-2x150_R1.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR30646119/HG008-T_HiC-Arima_ILMN-2x150_R1.fastq.gz.1", "size": "78101726185", "date": "2024-09-12 13:34:49", "md5": "5070d4243b15787173dd447c10789f0c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "HG008-T_HiC-Arima_ILMN-2x150_R2.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR30646119/HG008-T_HiC-Arima_ILMN-2x150_R2.fastq.gz.1", "size": "81585813332", "date": "2024-09-12 13:55:25", "md5": "c750278de3c365eaf776a74f01ad1a5a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]