Tumor cDNA Library Clone Number Justification

2015-01-13

azim58 - Tumor cDNA Library Clone Number Justification

Comments from Kathy
I have about 3*10^6 clones in my library (3,000 spots with 1,000 colonies
per spot). This is approximately how many would be needed for 3X
representation of a rare gene in a single cell.

There are about 20,000-30,000 genes in the genome. A single cell
expresses about 5-10,000 transcripts in one cell, but there is about
10-100 fold differences in expression level between genes. So about 10^4
clones would be necessary to detect 1 particular transcript. However,
since a rare transcript might occur 100X less often increasing the
coverage 100X from 10^4 to 10^6 increases the chances of discovering rare
clones. Then if you want 3X coverage this results in 3*10^6 clones.

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I looked at this again myself. (2-28-13)
There are about 50,000 transcripts in a cell. Most of the transcripts
occur at a copy number of 1-5 (What transcripts are found in a human
cell? - Genome Biology). If I have 3e6 clones how many times would a
transcript with one copy number be represented on average? 3e6/5e4 = 60

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