• What will be the minimum number of biological replicates (plant samples) and how many biological replicates are needed for RNA-Seq using HIseq ?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
One more question about the "replicate" definition; if you have a cDNA from a biological sample (for a RNA-seq experiment) and you use it into two PCR reactions with different barcodes (like the one you do before the Illumina run), the barcode1 and barcode2 samples from the same cDNA can be considered as "replicates".
Suppose you want statistical power in your data, and you want to test differential gene expression in programs like DESeq (where it wants replicates to check the so called "shot-noise"); in this case, can they be considered good "replicates"?
Thanks
Comment
-
Originally posted by cascoamarillo View PostOne more question about the "replicate" definition; if you have a cDNA from a biological sample (for a RNA-seq experiment) and you use it into two PCR reactions with different barcodes (like the one you do before the Illumina run), the barcode1 and barcode2 samples from the same cDNA can be considered as "replicates".
Suppose you want statistical power in your data, and you want to test differential gene expression in programs like DESeq (where it wants replicates to check the so called "shot-noise"); in this case, can they be considered good "replicates"?
Thanks
Comment
-
Yes, these replicates are only testing the reproducibility of the sequencing protocol, which is extremely high. Biological reproducibility is what we're interested in. I would just pool the data from technical replicates as a single biological replicate.
Comment
-
I would do no less than three independent biological replicates (i.e. RNA isolated from separate biological samples) of each condition. You can get meaningful results from 2 biological reps, but you are really restricting yourself by doing this, particularly on a HiSeq where you can easily multiplex and still get a lot of reads per sample even on a single lane.
Comment
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 07-25-2024, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
07-25-2024, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
160 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Comment