Need publicly available raw RNA-seq data generated by human cell lines

Question

[arta]

Hi,

I have done alternative splicing analysis using our in-house data which were paired-end (2 X 125 bp) human triplicate H322 and A431 cell lines. Now i want to compare my results with different lineages such as neural, mesenchymal or hematopoietic. Therefore i need raw (fastq) triplicate RNA-seq data from human cell lines which should be generated by same technology Illimuna and ~ 250 bp length. I checked GEO, SRA (from NCBI) and ArrayExpress (From EMBL) but i could not find what i was looking for. I know i have very restricted criteria but i will be glad if you know other databases or could be your published data.

[JJ]

Have you looked at the Encode data?

[arta]

I checked but that was not helpful (or i could not find what i was looking for).

Answer 1

[i.sudbery]

You could try the Cancer Cell Line Encylopedia (CCLE). The raw data is not so easy to find, but it is here. It is in the form of BAM files. If you want it fastq raw then you'll need to convert these back to fastq with samtools.

[arta]

Thanks for the link. However, the cell lines have only one replicate. But i will keep in my mind that link for the future.

Fortunately, I have found nature paper where they analyzed 675 cell lines with duplicates and we can find more info about data here.