Question: CCLE RNA-seq library protocol
0
gravatar for zju.whw
4.7 years ago by
zju.whw30
China
zju.whw30 wrote:

Hi, everybody!

I have downloaded some CCLE(Cancer Cell Line Encyclopedia) RNA-seq data from the CGHuB website. It is the public accessible data. this is their dataset browser https://browser.cghub.ucsc.edu/. But I can't find the information about the RNA-seq library protocol, such as polyA+ or not, strand-specific or not, paired-end or single-end? So is there anybody can tell me how to find these information or some useful materials or website?

Thank you, everyone.

rna-seq ccle • 4.5k views
ADD COMMENTlink modified 4.1 years ago by Sebastian Boegel460 • written 4.7 years ago by zju.whw30
3
gravatar for Sebastian Boegel
4.1 years ago by
Germany
Sebastian Boegel460 wrote:

Hi,

just stumbled over your post. I dont know, if that still helps:

"Large insert non-strand specific RNA Sequencing included plating, poly-A selection and cDNA synthesis, library preparation (400bp insert), sequencing (101bp paired reads) and a sample identification QC check. Non-strand specific RNA sequencing performed at the Broad Institute uses a large-scale, automated variant of the Illumina Tru Seq™ RNA Sample Preparation protocol (Illumina: TruSeq Protocol Info). An amount of 200 ng of total RNA is used for starting material. This method uses oligo dT beads to select mRNA from the total RNA sample. The selected RNA is then heat fragmented and randomly primed before cDNA synthesis from the RNA template. The resultant cDNA then goes through Illumina library prep (end repair, base 'A' addition, adapter ligation, and enrichment) using Broad designed indexed adapters for multiplexing. After enrichment, the samples are qPCR quantified and equimolar pooled before proceeding to Illumina sequencing with is done on the Illumina HiSeq 2000 or HiSeq 2500, with sequence coverage to 100M paired reads. All samples are electronically tracked through the process in real-time including reagent lot numbers, specific automation used, time stamps for each process step, and automatic registration. The entire process occurs in a 96-well format, and all pipetting is done by either Bravo or Mini Janus liquid handlers."

 

https://cghub.ucsc.edu/datasets/ccle.html

ADD COMMENTlink written 4.1 years ago by Sebastian Boegel460

This is what I want, thank you.

ADD REPLYlink written 4.1 years ago by zju.whw30

Just to confirm, so CCLE mRNA dataset is non-stranded, right?

ADD REPLYlink written 16 months ago by -_-740

That link to cghub/../ccle.html is "Not found" now, but the information is available on ArrayExpress: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2770/E-MTAB-2770.idf.txt

ADD REPLYlink written 6 months ago by sbridgett0
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