Non coding RNA expression data
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7.4 years ago
jack ▴ 940

Hi all,

 

I'm looking for database which contains expression levels of total RNAs.

I have tried TCGA, but it's mostly for protein coding and miRNAs.

Does anyone can help me with that ?

RNA-Seq sequencing gene expression • 2.5k views
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7.4 years ago

You can try GEO database.

 

Paste, for example, "Non coding RNA" in search field. Then, you can filter by "Non-coding RNA profiling by high throughput sequencing". Review results.

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Thanks for the great list. Actually, I am interested in investigating the correlation between specific lncRNA's expression and the mRNA expression of a list of genes. So far I found MiTranscriptome and TANRIC useful. I am interested in getting both lncRNA exp and mRNA exp in similar samples (for example: TCGA normal and cancer cell samples)

The first three are not accessible but thanks again for providing these info.

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7.4 years ago
Charles Plessy ★ 2.8k

Have a look at the FANTOM5 expression atlas. Expression is quantified at the level of transcription start sites, and is not restricted by a priori definitions of gene structures.  Only after peak calling, the expression peaks have been associated with overlapping or neighbor gene models (GENCODE, ...).

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7.4 years ago
h.mon 34k

modENCODE has transcriptional profiles from total RNA for D. melanogaster and C. elegans.

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7.4 years ago
verma ▴ 30

Hey Hii,

             Please use ChIPBase database and also you can try to use mirCoX database. It may help to sort your problem.

Regards,

Garima Verma.

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5.6 years ago
Saber HQ ▴ 60

As for Long non-coding RNAs expression, you can try TANRIC website

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