Availability of RNA-seq technical replicates

yumpe · 09-14-2020, 07:40 AM

Hi all,

I'm looking for RNA-seq datasets (from any of the popular short-read platforms) that contains more than two technical replicates per sample. I specifically need read counts, not normalized data, also preferably poly-A enriched RNA but I could use anything, and any organism will do. I can find plenty of read count data from duplicate technical replicates, but I'm looking for data with at least 3, but preferably as large number of technical replicates as possible. I wonder if anyone really dug into the reproducibility or RNA-seq in their hands and did 10 technical replicates from a given sample? Sorry, RNA-seq beginner here and don't know the field that well, so any and alll replies will be helpful.

Thank you!

GenoMax · 09-14-2020, 11:37 AM

No one does technical replicates since they don't add any value to the datasets. Are you looking for "biological" replicates?

yumpe · 09-15-2020, 01:55 PM

As it said in my original post, I'm looking for "technical" replicates.
Maybe I am one of the few people interested in the technical variability of a technique.
Still am, and grateful for any pointers.
Thanks!

GenoMax · 09-15-2020, 07:16 PM

You will need to look around to find such data. A library run on multiple lanes (which would be technical replicates) may just be concatenated into a single file for analysis and may not be reported specifically in papers.

I found this paper (which is not for RNAseq) but does contain technical replicates.

yumpe · 09-16-2020, 12:27 PM

Thanks GenoMax, appreciate your help.
I'm specifically looking for RNA-seq data.
I'll keep looking!

cmbetts · 09-16-2020, 02:55 PM

You might try to look at some of the method/kit comparison papers, or a paper describing a new library prep method. They often compare inter and intra assay performance of replicate inputs, usually Universal Human Reference RNA.

You'll likely only find older papers using technical replicates. The outcome of the early characterization experiments was that technical replicates are unnecessary, especially in comparison to the added value of biological replicates. They're essentially an elaborate way to burn money, but I'm sure Illumina would love you if you find an argument for them...

yumpe · 09-17-2020, 02:03 PM

Hi cmbetts,

My only interest is academic, trying to understand the variability of RNA-seq workflows as well as I can.

Best,

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09-14-2020, 07:40 AM	#1
yumpe Junior Member Location: San Francisco, CA, USA Join Date: Sep 2020 Posts: 4	Availability of RNA-seq technical replicates Hi all, I'm looking for RNA-seq datasets (from any of the popular short-read platforms) that contains more than two technical replicates per sample. I specifically need read counts, not normalized data, also preferably poly-A enriched RNA but I could use anything, and any organism will do. I can find plenty of read count data from duplicate technical replicates, but I'm looking for data with at least 3, but preferably as large number of technical replicates as possible. I wonder if anyone really dug into the reproducibility or RNA-seq in their hands and did 10 technical replicates from a given sample? Sorry, RNA-seq beginner here and don't know the field that well, so any and alll replies will be helpful. Thank you! __________________ -yumpe

09-15-2020, 01:55 PM	#3
yumpe Junior Member Location: San Francisco, CA, USA Join Date: Sep 2020 Posts: 4	As it said in my original post, I'm looking for "technical" replicates. Maybe I am one of the few people interested in the technical variability of a technique. Still am, and grateful for any pointers. Thanks! __________________ -yumpe Last edited by yumpe; 09-15-2020 at 01:58 PM.

09-16-2020, 12:27 PM	#5
yumpe Junior Member Location: San Francisco, CA, USA Join Date: Sep 2020 Posts: 4	Thanks GenoMax, appreciate your help. I'm specifically looking for RNA-seq data. I'll keep looking! __________________ -yumpe

09-17-2020, 02:03 PM	#7
yumpe Junior Member Location: San Francisco, CA, USA Join Date: Sep 2020 Posts: 4	Hi cmbetts, My only interest is academic, trying to understand the variability of RNA-seq workflows as well as I can. Best, __________________ -yumpe

09-14-2020, 11:37 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	No one does technical replicates since they don't add any value to the datasets. Are you looking for "biological" replicates?

09-15-2020, 07:16 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	You will need to look around to find such data. A library run on multiple lanes (which would be technical replicates) may just be concatenated into a single file for analysis and may not be reported specifically in papers. I found this paper (which is not for RNAseq) but does contain technical replicates.

09-16-2020, 02:55 PM	#6
cmbetts Senior Member Location: Bay Area Join Date: Jun 2012 Posts: 120	You might try to look at some of the method/kit comparison papers, or a paper describing a new library prep method. They often compare inter and intra assay performance of replicate inputs, usually Universal Human Reference RNA. You'll likely only find older papers using technical replicates. The outcome of the early characterization experiments was that technical replicates are unnecessary, especially in comparison to the added value of biological replicates. They're essentially an elaborate way to burn money, but I'm sure Illumina would love you if you find an argument for them...