Question: Publicly available RNA-seq data of neurons from human
1
gravatar for flsnike
2.4 years ago by
flsnike10
flsnike10 wrote:

Hi dear all, I have been recently searching for RNA-seq data of neurons that are primary cells from human, but not iPSC-derived neurons, and not single cell RNA-seq data. I searched SRA, ENCODE, and GEO database it seems the results are almost all iPSC-derived neuron .. Anyone can help me to find such RNA-seq data ? and can I use the RNA-seq data from brain tissues (say, frontal cortex) because there are some such RNA-seq data in ENCODE. Which part of brain tissues are enriched in neurons? Thanks in advance!

rna-seq sequence • 1.5k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by flsnike10

Take a look here to see if there are any datasets you can use: http://www.gtexportal.org/home/

ADD REPLYlink written 2.4 years ago by genomax67k

GTEx has brain data, but not specifically neuron data.

ADD REPLYlink written 2.4 years ago by i.sudbery4.5k
2
gravatar for WouterDeCoster
2.4 years ago by
Belgium
WouterDeCoster39k wrote:

and can I use the RNA-seq data from brain tissues (say, frontal cortex) because there are some such RNA-seq data in SRA. which part of brain tissues are enriched in neurons?

To answer this part of the question: brain tissue is highly heterogeneous and contains many many cell types. Therefore it's important to choose the right part of the brain depending on your biological hypothesis. In addition, you need to make sure that the tissue-extraction was performed carefully and there is minimal contamination of neighbouring brain regions. It's a mess.

ADD COMMENTlink written 2.4 years ago by WouterDeCoster39k
2
gravatar for A. Domingues
2.4 years ago by
A. Domingues2.0k
Mainz, Germany
A. Domingues2.0k wrote:

I have used this repositive in the past to search for datasets. If I am not mistaken it aggregates data from other repositories, but makes the search quite fast and efficient (compared to GEO for instance). It required a (free) registration though.

A quick search using your keywords and it seems that there is something out there is out there from native tissue. However, keep in mind that there won't be a lot. A reason might be the ethical restrictions accessing human tissues, and brain is even more difficult to get without causing damage to the patient. Alternatively, tissue is obtained post-mortem.

That said, here are some datasets that might be of interest:

1 - RNA-Seq analysis of human fibroblasts, induced neurons and cortex from donors of several ages

2 - small RNA-seq from frontal cortex (ENCSR000AFS)

There are more, so if you are willing to register and replicate the results, my search terms were "RNA-seq cortex".

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by A. Domingues2.0k

Thank you so much for the nice data resource site. I still cant find the data of interest, and as mentioned by WouterDeCoster, I am not sure whether the RNA-seq of cortex can be used due to brain tissue heterogeneity.

ADD REPLYlink written 2.4 years ago by flsnike10
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