Adapter enrichment and extension

[arussell]

Hello,

I am new to RNA-seq, and am working though the details of how the process works. These are the adapters I am working with, that need to be incorporated into the cDNA.

PE1: 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3'

Index: 5' CAAGCAGAAGACGGCATACGAGATNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGAT 3' (NNNN represents barcode nucelotides)

To the best of my knowledge, the flow cell sequences are:

p5: 5' AATGATACGGCGACCACC GA 3'
p7: 5' CAAGCAGAAGACGGCATACGAGAT 3'

However, I'm not sure if that means those are the sequences that the adapters need to contain, or if those are the binding site sequences and the cDNA needs to contain the complements. Does this mean that my adapterized cDNA sequences will look like scenario 1, 2, or 3?

1)

5' PE1 --- cDNA --- Index 3'
3' PE1(complement) --- cDNA --- Index (complement) 3'

2)

5' PE1 --- cDNA --- Index (complement) 3'
3' PE1 (complement) --- cDNA --- Index 3'

3)

5' PE1 --- cDNA --- Index 3'
3' Index --- cDNA --- PE1'

**In this case, are the PE1 and Index sequences partially complementary?

Thank you!