ChIP-seq sequence data sources

2.2 years ago by

VY • 120

London

VY • 120 wrote:

If you're looking at nucleosome positioning you probably need ATAC-seq data and/or DNAse -seq data etc. ChIP-seq won't give you that unless you are looking at a specific nucleosome remodeling protein (or any protein for that matter). Also specifying from what bovine tissue you want would be most helpful. People generally don't sequence nucleic acids from the whole eukaryotic organism.

You can download most SRA files from published data if authors of a specific paper have made it available. If you read this post here on biostar it is pretty detailed about how to go about doing that.

https://www.biostars.org/p/111040/

Best wishes, Val

ADD COMMENT • link written 2.2 years ago by VY • 120

Once you find your data, this is how to load it into Galaxy. Some sources have targetted tools, see the tool group Get Data.

https://wiki.galaxyproject.org/Support#Loading_data

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

hello dear val in my project To uncover the genes involved in the development of mastitis(bovine), a meta-analysis using publicly available GEO microarray datasets was performed. The metaDE package in R language was used to do meta-analysis. 32 genes differentially expressed genes (DEGs) were obtained from meta analysis. Using Fasta format for these genes did predict nucleosome positioning by( https://genie.weizmann.ac.il/ software/nucleo_prediction.html). Now I want to use the chip-seq information for these genes doing predict nucleosome positioning. please tell me what I have to do it? thanks

2016-10-03 18:12 GMT+03:30 VY on Galaxy Biostar notifications@biostars.org :

ADD REPLY • link written 2.2 years ago by z.biranvand1983 • 0

Hello, again, to my knowledge, ChIPseq will not predict nucleosome spreading. Off the top of my head the only way you could INFER that from ChIPseq is if you have ChIP data done on Polycomb and/or Trithorax proteins that are known to compact or relax chromatin (e.g Ring1B and MLL1 respectively -please note that there are more) or ChIPseq datasets from chromatin remodelers that are known to interact with chromatin in an obstructive or permissive way. (e.g CHD group of proteins).

Another way to infer possible chromatin accessibility is by looking at permissive or repressive histone marks. Again though, none of what I've said will give you clear information on your nucleosome spreading at given regions. If you do have access to such data, from the cells you are working on or a closely related tissue, you can import them into galaxy as Jennifer has said above in her comment.

ADD REPLY • link written 2.2 years ago by VY • 120

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