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colorectal cancer ribo-seq data
23-May-2015, 01:19 PM
Post: #1
colorectal cancer ribo-seq data
Hello!

I´m new in the filed of NGS and specially in ribosome profiling. But i will start my PhD in this area focusing mainly in colorectal cancer cell lines. so my question is if there are some ribo-seq data in colorectal cancer and if there are can someone help me to reach this information?

thank you so mutch for your kind attention!
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25-May-2015, 08:52 AM (This post was last modified: 25-May-2015 08:55 AM by audrey.)
Post: #2
RE: colorectal cancer ribo-seq data
Hi Joana,

There is ribo-seq data on HCT116 cells available on NCBI GEO datasets GSE58207 ( http://www.ncbi.nlm.nih.gov/geo/query/ac...c=GSE58207 ).

This data is not yet in GWIPS-viz. However, the bedGraph files provided at the bottom of the link above can be uploaded as custom tracks in GWIPS-viz which will allow you to explore the alignments.

Alternatively, if you wish to align the raw data using RiboGalaxy, from within RiboGalaxy click on the on the EBI SRA ENA SRA LHS panel under Get Data and enter GSE58207 in the search box. Click on the SRP042937 link and then on the File 1 option under Fastq files (galaxy). The raw fastq file will be copied directly to RiboGalaxy and can then be processed and aligned.

Hope this helps.
Regards,
RiboGalaxy team
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25-May-2015, 09:44 AM
Post: #3
RE: colorectal cancer ribo-seq data
Goof morning!

Thank you very much! You help me a lot with this information, is exactly what I need! Smile

Best regards,
Joanaa Silva
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