Question: RNA-seq data from CCLE - where are the details?
0
gravatar for fr
2.2 years ago by
fr130
fr130 wrote:

I'd like to use the RNA-seq data from CCLE found at https://portals.broadinstitute.org/ccle/data. Where may I find more information about the methods that were considered to process the data?

Thanks in advance

rf

rna-seq ccle gene • 3.9k views
ADD COMMENTlink modified 2.2 years ago by Kevin Blighe61k • written 2.2 years ago by fr130
0
gravatar for Kevin Blighe
2.2 years ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

E ai cara, check the original publication: The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity

In particular, look at Supplementary Material 1 (Word doc) - it has information on each of the following:

Supplementary Methods

1. Cell line selection and annotation

2. DNA and RNA extraction

3. Genomic characterization
   SNP Arrays:
   DNA identity analysis by mass spectrometric SNP genotyping

4. Cell line identity validation by SNP genotyping

5. Gene set activity scores

6. Cell line-to-primary tumor comparison
   Copy-number comparison:
   Expression comparison: 
   Mutation-rate comparison

7. Pharmacological characterization

8. Prediction of drug response
   8.1. Sensitivity prediction using regression analysis
   8.2. Sensitivity prediction using categorical analysis

9. AHR validation experiments
   Cell lines and cell culture conditions
   Lentivirally delivered short hairpin RNA
   Immunoblot analysis:
   Analysis of mRNA expression by quantitative RT-PCR (qRT-PCR)
   Growth curves
   Pharmacologic growth inhibition curves

10. Data sharing/release
All raw and processed data are available at the CCLE website: www.broadinstitute.org/ccle In addition, the website offers direct links to data visualization tools such as IGV39, as well as genepattern-based40 analysis tools for expression and copy-number class comparison analyses.
ADD COMMENTlink written 2.2 years ago by Kevin Blighe61k

Ola'! Many thanks for your response! Unfortunately, they do not mention the procedures for RNAseq processing, and perhaps they have changed them in the last 6 years?

ADD REPLYlink written 2.2 years ago by fr130

The RNAseq data has been published since the release of the paper.

ADD REPLYlink written 2.2 years ago by i.sudbery8.2k

@i,sudbery thanks. Do you have the reference for the publication?

ADD REPLYlink written 2.2 years ago by fr130
1

Take a look here: CCLE RNA-seq library protocol

ADD REPLYlink written 2.2 years ago by Kevin Blighe61k

This is great, thanks so much!

ADD REPLYlink written 2.2 years ago by fr130
1

De nada amigo.

ADD REPLYlink written 2.2 years ago by Kevin Blighe61k

Where can I find information on how they analyzed the RNA-seq data? Thank you!

ADD REPLYlink written 6 months ago by ablazier20

Read the supplementary material.

ADD REPLYlink written 6 months ago by Kevin Blighe61k
1

Thanks, Kevin. Just for an updated reference, I found the RNA-seq analysis info as part of this paper: Next-generation characterization of the Cancer Cell Line Encyclopedia

ADD REPLYlink written 5 months ago by ablazier20

Hi Kevin,

Where can I find CCLE Breast RNA-Seq data (not microarray) PAM50 Subtype information?

Thank you

ADD REPLYlink written 2.1 years ago by Vasu450

Hello my friend. Where have you looked already? The CCLE ma not report the PAM50 subtypes.

ADD REPLYlink written 2.1 years ago by Kevin Blighe61k

I have seen that it is reported in this paper [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001206/#MOESM1] But it is based on microarray data. What I need is for RNAseq data.

ADD REPLYlink written 2.1 years ago by Vasu450

I see, but those authors appear to have done the work on their own. That is, you extract the PAM50 genes from the data and then perform some clustering analysis in order to see how your samples are grouped based on the PAM50 genes. PAM50 is just a list of genes, after all. One can explore the utility of the signature in any expression dataset.

If you just need to know the genes, then take a look here: Where To Download Pam50 Gene Set?

ADD REPLYlink written 2.1 years ago by Kevin Blighe61k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1121 users visited in the last hour