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  • Joann
    replied
    Three colon cancer cell lines represented in patent literature found at USPTO are RKO, SW480 and SW620, therefore they would be most likely subjected to pharmaceutical industry level characterization and quite possibly outside published academic literature.

    Leave a comment:


  • krobison
    replied
    Links therein are supposed to point at the data. It is not rare for patient data to be protected by additional rules that can be challenging to navigate, so good luck.

    Comprehensive molecular characterization of human colon and rectal cancer.
    Cancer Genome Atlas Network.
    Collaborators (326)
    Abstract
    To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase ε (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.

    Leave a comment:


  • jimmybee
    replied
    EBI, DDBJ, 1000 genomes, there are many. Google is your friend

    Have you tried looking for an exome sequencing paper and perhaps looking for where the sequences are stored?

    Leave a comment:


  • desmo
    replied
    There are other database of sequences rather than NCBI?

    Leave a comment:


  • desmo
    started a topic Available colon cancer cell line?

    Available colon cancer cell line?

    Does anyone know where I can find an available exome of a colon cancer cell line?
    I've tried a search on NCBI (sra) but i didn't find nothing for this specific task.
    Thanks in advance to everyone

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  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM

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