Dear all,
I have a question to ask about multiplexing with Illumina Hiseq (I can have 150-200 Million reads per lane). I have 12 samples from 3 different conditions (each has 4 biological replicates, mouse cell culture):
control samples (C1, C2, C3, C4)
shRNA-1 samples (A1, A2, A3, A4)
shRNA-2 samples (B1, B2, B3, B4)
I plan to put 4 samples in each lane, then I have 3 lanes (save some money). I am not sure how should I choose the samples in each lane, either put 4 replicates in the same lane? or do a combination of different groups like:
Lane 1: C1, C2, A1, B1
Lane 2: C3, A2, A3, B2
Lane 3: C4, A4, B3, B4
And another question about single end and paired end sequencing? I am mostly interesting in the differential gene expression, not that into splicing or SNP. The core facility provides singe end 50 bp/100 bp and paired end 50 bp/100 bp, would single end 50 bp be enough for my purpose?
Thanks a bunch for your advice!
Wei
I have a question to ask about multiplexing with Illumina Hiseq (I can have 150-200 Million reads per lane). I have 12 samples from 3 different conditions (each has 4 biological replicates, mouse cell culture):
control samples (C1, C2, C3, C4)
shRNA-1 samples (A1, A2, A3, A4)
shRNA-2 samples (B1, B2, B3, B4)
I plan to put 4 samples in each lane, then I have 3 lanes (save some money). I am not sure how should I choose the samples in each lane, either put 4 replicates in the same lane? or do a combination of different groups like:
Lane 1: C1, C2, A1, B1
Lane 2: C3, A2, A3, B2
Lane 3: C4, A4, B3, B4
And another question about single end and paired end sequencing? I am mostly interesting in the differential gene expression, not that into splicing or SNP. The core facility provides singe end 50 bp/100 bp and paired end 50 bp/100 bp, would single end 50 bp be enough for my purpose?
Thanks a bunch for your advice!
Wei
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