Woody Lin

12 Questions 47 Answers 0 Followers

Questions related from Woody Lin

Can eQTL be validated by wet-lab experiments?

eQTL = Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in expression levels of mRNAs. In other words, a SNP regulating RNA expression level of a gene. Is...

12 December 2017 4,750 3 View

Is there a quick assay that tells the rate of mutation accumulation of a cancer cell line in different time points?

Except using illumina's sequencing. I am looking for a cheap and quick essay that can estimate the rate of mutation accumulation.

03 March 2015 8,322 0 View

SEQC project for DNA-Seq to estimate the coverage for low abundant mutations - any thoughts?

Dear all, SEQC has published a nice paper to better improve our expectations about RNA-Seq data. I am wondering if SEQC would do a similar assessment for DNA-Seq such as somatic...

09 September 2014 2,232 2 View

Is the RNA degradation rate of frozen normal tissue in -80 much faster than tumor tissue?

I noticed that frozen normal tissues very often have much lower RIN values (from bioanalyzer) while matched tumor tissues still have pretty good RIN values. I suspect that it is because the...

08 August 2014 9,421 4 View

Where are the references of TTN (titin) mutations in hepatocellular carcinoma?

Dear all, I have been reading a review article published on Nature Review Clinical Oncology in 2013. In the paper entitled "Mutational landscape of HCC", I noticed that TTN was labeled as a gene...

07 July 2014 8,931 8 View

What can I do with Cancer Exome-Seq data without matched normal?

Dear scientists, I am aware that tumor exome-seq data without a matched normal will have difficulty for distinguishing somatic and germline mutations. I aim to find "important" somatic mutations...

07 July 2014 9,781 7 View

Is there a method to extract tumours and adjacent normal tissues from mice multiple times?

I am wondering if there is a method for dissecting adjacent normal and tumor samples from living mice without sacrificing the mouse? I hope to study the tumor evolution at multiple time points...

05 May 2014 4,794 4 View

Would RNA quality/quantity be good enough for sequencing when the liver tumor samples are frozen and sliced?

One of my colleague thinks that the RNA quality should be fine for those cryo-sliced liver tumor samples. We just need to use more sliced samples to get enough RNA. Is this correct?

04 April 2014 9,348 5 View

Does anyone know the approximate price for TruSeq on MiSeq?

For example, stem cell panel contains 100 genes. How much would it cost for getting the 100 genes from 100 samples? Price of Targeted RNA Fixed Panels of Illumina TruSeq.

12 December 2013 6,135 2 View

Where do I find the number of common genes between two species?

In trees of life, people have been using the degree of conservation to assign the branches. I am wondering where I can look up for the numbers representing the diversity or commonality between two...

11 November 2013 5,130 6 View

Why are hemoglobin genes very often downregulated in cancers?

I found that mRNA levels of hemoglobin genes are downregulated very often in cancers (attached figure). I have checked Google and Wikigene, but I couldn't find any review article giving it an...

11 November 2013 8,262 8 View

Can metabolomics (LC-MS/MS) distinguish whether amino acids were from metabolites or proteins that are not extracted?

I have liver and serum results from metabolomics analysis. Some of the differential signals were identified as amino acids. I am curious whether the amino acids originated from actual metabolism...

01 January 2013 3,400 9 View