Cancer Cell Line Exome Sequencing
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001000978 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genomic characterisation of a large series of cancer cell lines.
| EGAD00001001039 | EGA
Project description:Genomic characterisation of a large series of cancer cell lines.
| EGAD00001001357 | EGA
Project description:Genentech cell line exome study. A wide variety of cell lines were sequenced.
| EGAS00001002554 | EGA
Project description:Genomic and proteomic data were integrated into the proteogenomic workflow to identify coding genomic variants of Human Embryonic Kidney 293 (HEK-293) standard cell line at the proteome level. Shotgun proteome data published by Geiger et al (2012) and obtained in this work for HEK-293 were searched against the customized genomic databased generated using exome data published by Lin et al (2014). 54 unique variants out of ~1,200 coding variants annotated in the exome were found at the proteome level. 27 of them were validated by two search engines, X!Tandem and Andromeda. 16 (60%) of those validated variants were confidently identified in both own and published proteome datasets. Some of the variants found belonged to widely known genomic polymorphisms originated from the germline, while others are more likely to result from somatic mutations. Notably, the peptide subsets identified by only one, or the other search engine were enriched by the sequences with miscleavages. This can be due to the large presence of false-positive hits in these subsets that is especially true for the subset of variant peptides. High-resolution mass-spectra of HEK-293 cell line were deposited to ProteomeXchange repository, project accession PXD002613.
2016-07-22 | PXD002613 | Pride
Project description:Agilent whole exome hybridisation capture will be performed on genomic DNA derived from renal cancer cell lines and matched normal DNA from the same patient. Illumina GA sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.
| EGAS00001000179 | EGA
Project description:HT-29 cells were barcoded using the CloneTracker lentiviral barcode library and then dabrafenib resistant derivatives of these cell lines were established, respectively. Five million barcoded HT-29 cells were seeded into 15 cm cell culture dishes. When the cells reached confluency, two million cells per dish were seeded into four different 15 cm dishes (DMSO Control, Replica A, B, C) and two million cell pellets were stocked as initial cell population. Harvesting used medium through the experiment was performed at monthly intervals. Barcoded HT-29 cell line replicates A, B, and C were treated with 2XIC50 (199.6 nM) of dabrafenib concentration for the duration of 3 months.Barcoded data can be accessed via accession code E-MTAB-13018. Whole exome sequencing of dabrafenib-resistant A replicate and DMSO control cell lines were carried out.
2023-09-06 | E-MTAB-13338 | biostudies-arrayexpress
Project description:Genomic and proteomic data were integrated into the proteogenomic workflow to identify coding genomic variants of Human Embryonic Kidney 293 (HEK-293) standard cell line at the proteome level. Shotgun proteome data published by Geiger et al (2012) and obtained in this work for HEK-293 were searched against the customized genomic databased generated using exome data published by Lin et al (2014). 54 unique variants out of ~1,200 coding variants annotated in the exome were found at the proteome level. 27 of them were validated by two search engines, X!Tandem and Andromeda. 16 (60%) of those validated variants were confidently identified in both own and published proteome datasets. Some of the variants found belonged to widely known genomic polymorphisms originated from the germline, while others are more likely to result from somatic mutations. Notably, the peptide subsets identified by only one, or the other search engine were enriched by the sequences with miscleavages. This can be due to the large presence of false-positive hits in these subsets that is especially true for the subset of variant peptides. High-resolution mass-spectra of HEK-293 cell line were deposited to ProteomeXchange repository, project accession PXD002613.
2017-03-28 | MSV000080712 | MassIVE
Project description:Two common sources of DNA for whole exome sequencing (WES) are whole blood (WB) and immortalized lymphoblastoid cell line (LCL). However, it is possible that LCLs have a substantially higher rate of mutation than WB, causing concern for their use in sequencing studies. We compared results from paired WB and LCL DNA samples for 16 subjects, using LCLs of low passage number (<5). Using a standard analysis pipeline we detected a large number of discordant genotype calls (approximately 50 per subject) that we segregated into categories of "confidence" based on read-level quality metrics. From these categories and validation by Sanger sequencing, we estimate that the vast majority of the candidate differences were false positives and that our categories were effective in predicting valid sequence differences, including LCLs with putative mosaicism for the non-reference allele (3-4 per exome). These results validate the use of DNA from LCLs of low passage number for exome sequencing.
| S-EPMC3812417 | biostudies-literature
Project description:PEO1 is part of the PEO/PEA series of ovarian cancer cell lines established in 1988 from progressive samples from three separate cases of ovarian cancer (Langdon et al., 1988).
2011-06-30 | GSE29256 | GEO
Project description:Genomic changes in low and highly metastatic A549 cells were analyzed by 500K SNP arrays. A large number of genomic alterations were present in A549 cells but no significant differences were observed between the low or highly metastatic A549 cell lines.
2013-02-21 | GSE44549 | GEO