Recent advances in rna seq include single cell sequencing and in situ sequencing of fixed tissue. The purpose of our study was to identify novel pathways that could be. Im not looking for rna seq on patient cells like in tcga because they contain many other mutations so the cancer formation is hard to be attributed to a particular gene mutation. Its purpose is to help us track usage for reports to our funding agencies and for insights into improving the portal. Oct 27, 2011 sample collection and rna seq preparation.
Here, we used rna sequencing rna seq to compare the transcriptomes of nonsmall cell lung cancer nsclc and normal lung tissues and to investigate expression in lung cancer tissues. Analysis of the prostate cancer cell line lncap transcriptome. I have downloaded some ccle cancer cell line encyclopedia rna seq data from the cghub website. Provides a compilation of gene expression, chromosomal copy number, and massively parallel sequencing data from human cancer cell lines. Analysis of public rnasequencing data reveals biological. Projects such as the cancer cell line encyclopedia ccle 5 and md anderson cell lines project mclp 6 generated a variety of cancer cellline rnaseq. Introduction colorectal cancer crc alone accounts for close to 10% of all cancer cases worldwide, and is a heavy burden on human health and economy. Comprehensive computational framework for the assessment of tumor suppressor status.
Nextgeneration sequencing and advances in realtime pcr qpcr throughput have revolutionized the way differential gene expression is analyzed, including variability between gene alleles and differently spliced transcripts, noncoding rnas, posttranscriptional mutations and editing, and gene fusions. Single cell rnaseq reveals the potential risk of different human organs vulnerable to 2019ncov infection. Our comprehensive product offerings support multiple cancer research applications, including studies of dna, rna, epigenetics, and more. Mar 29, 2012 the cancer cell line encyclopedia project was enabled by a grant from the novartis institutes for biomedical research. Singlecell rna sequencing study of melanoma national. Sep 29, 2006 by resequencing the mrna products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell. Pdf highthroughput rna sequencingbased virome analysis of. This study demonstrated the efficacy of parp inhibition in sensitising the radiation resistant pc3 prostate cancer cell line to the effects of rt. Cancer cell line encyclopedia five key discoveries seven. Status obtained by integrative analysis of sequencing, expression and cn datasets. In this study, rna seq data of 474 cancer related genes known tsgs and oncogenes and their corresponding isoforms were obtained from 69 human cell line samples. Rna sequencing of mcf7 breast cancer cells identifies novel. Experiment cancer cell lines from the cancer cell line encyclopedia rnaseq mrna baseline.
I have downloaded some ccle cancer cell line encyclopedia rnaseq data from the cghub website. Here, we analyze the transcriptome of csc and noncsc subpopulations by rna seq to identify new potential therapeutic. However, the majority of patients will eventually show resistance to antiangiogenesis therapies. Cancer stem cells cscs are hypothesized to account for therapeutic resistance, suggesting that cscs must be specifically targeted.
Additional funding support was provided by the national cancer institute m. Rna sequencing has opened new avenues for the study of transcriptome composition. Wgs and targeted sequencing of 503 cell lines, we also assessed tert. Rna seq can also be used to determine exonintron boundaries and verify or amend previously annotated 5 and 3 gene boundaries. After downloading rnaseq data for 935 cell lines from the cancer cell line encyclopedia ccle, transcriptlevel abundance was quantified using salmon 1. To this end, we conducted wholegenome and transcriptome sequencing on three tumor cell lines a431, u251mg and u2os for which there is. Prior to rna seq, gene expression studies were done with hybridizationbased microarrays. Rnaseq of 934 human cancer cell lines from the cancer cell line encyclopedia. Raw bam files used to generate this data is avaliable at gdc. Long noncoding rnas lncrnas have recently emerged as critical molecules in the development, cell growth, apoptosis, and metastasis of crc. The processed sequencing dataset was then analyzed to infer and understand the network of pairwise interactions amongst all the genes. Table 2 comparison of snvs identified in cell lines using rnaseq data.
Using pairedend rna seq samples from 1,082 cancer cell lines, we determined the 4digit hla class i and class ii type and hla expression using the tool seq2hla 6, 15. Genentech authenticated cell lines contain a consolidated list of 3587 cell lines, of which we had access to rnaseq data for more than 900 cell lines covering most of the commonly used cell lines. Oct 27, 2009 here, we briefly describe technical issues accompanying rna seq data generation and analysis, highlighting differences to arraybased approaches. Comprehensive analysis of the genome transcriptome and. Cell lines are commonly used as in vitro models for cancer and drug testing. Cancer genomics solutions for multiple research applications. Transcriptome analysis of intermixed human and mouse cells has, however, frequently relied on the need to separate the two cell populations prior to transcriptome. The resulting 935 quantification files, named by sample id, have 4 columns for ensemble gene id, length, number of reads, and transcripts per million tpm. The mutational status of more than 1,600 genes is determined by targeted massively parallel sequencing, followed by removal of variants likely to be germline events.
However, it is still not clear to what extent this diversity prevails when considering the relative abundances of different transcripts from the same gene. The development of reliable gene expression profiling technology increasingly impacts our understanding of lung cancer biology. Dec 29, 2016 long rnas are first converted into a library of cdna fragments through either rna fragmentation or dna fragmentation. Aug, 2015 decoding transcriptional effects of experimental tissuetissue or cellcell interactions is important. Secondly, the cancer rna seq data were generated using different experiment designs, sequencing platforms, cdna library protocols, genetic backgrounds cell lines or patients and so on. Background the only therapeutic options that exist for squamous cell lung carcinoma scc are standard radiation and cytotoxic chemotherapy. Cancer cell line encyclopedia ccle the cgc knowledge center.
Hela is an immortal cell line used in scientific research. Expression atlas rna seq data set have different sizes, which can influence the power of statistical analysis. Inferred copy number variations from the single cell rna seq data separate carcinoma cells from non cancer cells. Rnaseq of 934 human cancer cell lines from the cancer. Recent advances in rnaseq include single cell sequencing and in situ. Decoding breast cancer tissuestroma interactions using. Acceptance of the terms of access is a prerequisite for using this site. Despite recent advances in our understanding of the causes and in the treatment of primary tumors, the biological and molecular mechanisms underlying the metastasis of cancer. In this study, we employed a more sensitive rna sequencing rna seq to compare. Padi2 mrna expression levels across 57 breast cancer cell lines were measured by rnaseq. Systematic evaluation of rna sequencing kits using cancer cell. When available, hla typing data from literature are integrated. Identification of gene fusion transcripts by transcriptome.
Linc00659, a long noncoding rna, acts as novel oncogene in. Breast cancer researchers use cell lines to model myriad phenomena ranging from dna repair to cancer stem cell phenotypes. Cancer transcriptome sequencing captures both coding and noncoding rna and provides strand orientation for a complete view of expression dynamics. It is the oldest and most commonly used human cell line. I am looking for databases that has the rna seq data for different cancer cell lines and control cell lines. The resulting collection encompasses 36 tumor types. Pdf highthroughput rna sequencingbased virome analysis. Dec 15, 2014 a good correlation was observed between the ddpcr and the rnaseq three replicates in general spearman r 0.
Home about data contact login ccle logo broad logo. Rna sequencing identifies novel markers of nonsmall cell. Singlecell rnaseq enables comprehensive tumour and immune. Mutation data for individual cell lines is viewable. Tumor suppressors status for 69 tumor suppressors across 799 cancer cell lines. Background accumulating evidence supports that tumor growth and cancer relapse are driven by cancer stem cells. Cancer rna seq enables detection of strandspecific information, an important component of gene regulation. The number of cases for each cancer type denoted by 24letter codes present in ccle, viewed using the cancer genomics cloud. Variation within the complex ecosystem of a tumor may explain why targeted treatments benefit some patients more than others, and new technologies now allow researchers to look closely at the role of each component of a tumor. Nextgeneration characterization of the cancer cell line encyclopedia. Singlecell rna sequencing reveals evolution of cancer cell. Nov 20, 2015 to our knowledge, this is the largest catalog of hla type and expression annotated cancer cell lines.
Mar 10, 2018 colorectal cancer crc is one of the most common cancers and causes of cancer related death worldwide. Thus, single cell rna seq is a powerful approach for identifying unique tumor cell specific gene expression profiles which could facilitate the development of optimized clinical anti cancer strategies. In patients with crc, metastasis is a crucial problem that leads to treatment failure and is the primary cause of the lethality of colon cancer. Recently, the national cancer institute began exploring opportunities to work with molecular data in cloudcomputing environments. A bioinformatics approach to identify novel long, noncoding rnas. Assessing breast cancer cell lines as tumour models by. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts.
Integrative analysis provides a more reliable status than sequencing alone. Rnaseq, also called rna sequencing, is a particular technologybased sequencing. Sequencing adaptors blue are subsequently added to each cdna fragment and a short sequence is obtained from each cdna using highthroughput sequencing technology. National cancer institute not all tumor cells are made equal. Tumor suppressors status in cancer cell line encyclopedia. Nevertheless, the characteristics of these cells are still poorly understood. I am trying to find a database which has rna seq data for cancer cell lines transformed from normal cells by specific oncogenes or mutated tumor suppressors. The idea of a large scale drug treatment dataset was brought to fruition in 2012 with the publication of the cancer cell line encyclopedia, which collected data on nearly human tumor cell lines, cancer cells which have been coaxed to grow indefinitely in the lab. Pharmacogenomic agreement between two cancer cell line data sets.
Furthermore, we performed the same comparison analysis on rnaseq samples from encode, roadmap epigenomics, and cancer cell line encyclopedia ccle. Niacinamide is a known inhibitor of parps which are involved in the repair of singlestranded breaks ssb. We studied the transcriptomes of five brca1mutated breast cancer cell lines one of which is a matched lymphocyte cell line, three brca1mutated primary tumors, two secretory breast ductal carcinoma primary tumors sec1 and sec2 and one nontumorigenic breast epithelial cell line table 1. Metastasis is the main cause of treatment failure and death in cancer patients.
Though appropriate, and even requisite, for many studies, the suitability of cell lines as tumour models has come into question owing to possibilities of tissue culture artefacts and clonal selection. Jonathan goke generated nanopore data from six cell lines and evaluated nanopore methods for producing fulllength rna sequences via direct rna sequencing. Gene expression profiling of liver cancer stem cells by rna. Padi2 is most highly expressed in the luminal lines 2629 above background.
In addition, using the wgs and rnaseq data, we now include. Rna sequencing reveals upregulation of runx1runx1t1 gene. In the bottomright part of the project information box, click copy project. At a single cell resolution, carcinoma cells display common signatures within the. So youll be better able to perform the worldclass research you strive forwith the goal of uncovering new insights into the biology of cancer that can lead to meaningful advances in personalized medicine. In the present study, we performed deep rna sequencing rnaseq as an unbiased highthroughput technique for comprehensive transcriptome analysis in er. Padi2 levels are shown relative to all other genes in each cell line. Cancer cell line encyclopedia ccle the cgc knowledge. Rna sequencing analysis reveals interactions between breast. Gene methylation can also be visualized through a bubble map. Jun 19, 2015 single cell rna seq on viable pdx cells identified a candidate tumor cell subgroup associated with anti cancer drug resistance. Singlecell rnaseq supports a developmental hierarchy in. The dataset also contained a dcis cell line that is unavailable in ccle and other rnaseq datasets from breast cancer cell lines 31. We present the utility of massively parallel sequencing by synthesis for profiling the transcriptome of a human prostate cancer cell line, lncap, that has been treated with the synthetic androgen, r1881.
Each cell line was genetically characterized through a series of highthroughput analyses at the broad institute. Aug 09, 2018 the researchers first began to suspect that these cell lines evolve when they reanalyzed sequencing data from 106 lines housed in two large collections. It has been estimated that in total 694,000 people died from crc in 2012 1. Access the ccle public project by selecting cancer cell line encyclopedia ccle from public projects in the top navigation bar. We have generated and stored variant profiles for these 900 plus cell lines for comparison and will keep updating the database as we have access to rnaseq data for additional cell lines. Transcriptome analysis of human tissues and cell lines.