referring to this quote from an article about predicting methylation states:

"Because of the small amounts of genomic DNA starting material per cell, single-cell methylation analyses are intrinsically limited by moderate CpG coverage"

can you please explain it to me?

What is exactly starting material? and why it's small per cell?

  • $\begingroup$ Please try to find the meaning of common English scientific phrases by an internet search. And think about how big a single cell is and how much DNA there would be in it. $\endgroup$ – David Jun 5 '18 at 20:44
  • $\begingroup$ Can you please link to the document you're citing from? Without a context, it sounds rather difficult to interpret this sentence. $\endgroup$ – Remi.b Jun 5 '18 at 22:31
  • $\begingroup$ link.springer.com/article/10.1186/s13059-017-1189-z $\endgroup$ – Samir Naseer Jun 7 '18 at 11:20

The comparison the authors are making is between bulk and single-cell sequencing. Currently, single-cell sequencing is becoming very popular as it allows much finer grain analyses of the biological expression. For example, tumor sub-populations can be determined.

However, single-cell analysis lose a great deal of genomic material, causing the resultant measures (expression most often) for each cell to have very minimal and sparse values.

Therefore the starting material is simply the DNA in each cell, which is limited by the single-cell process.

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  • $\begingroup$ You write "the starting material is simply the RNA in each cell". Perhaps you can explain how you can measure DNA methylation starting with RNA. The poster actually quotes what the starting material is: "genomic DNA" but appears unfamiliar with the English expression "starting material". As for "CpG coverage" it would appear that both his scientific knowledge and his English is deficient. But you ignore that part of his question. $\endgroup$ – David Jun 6 '18 at 19:07
  • $\begingroup$ I know the English meaning of the words "starting material". My question: what is that starting material? and why it's not enough? $\endgroup$ – Samir Naseer Jun 7 '18 at 11:24
  • $\begingroup$ specifically, is CpG coverage the number/percentage of C-G sites covered in sequencing? or it's something related to methylation? $\endgroup$ – Samir Naseer Jun 7 '18 at 11:26
  • $\begingroup$ CpG coverage is a general term, but thinking about it as the fraction of methylated CpG sites over the total number of CpG sites is accurate. To get the number of CpG sites, accurate sequencing of the genome needs to be accomplished. As I tried to explain, the single cell method limits the amount of DNA (edited the answer to be correct) able to be sequenced, and therefore the number of CpG sites is not well known, and the CpG coverage as well. $\endgroup$ – user42909 Jun 7 '18 at 12:17
  • $\begingroup$ Also the question states "What is exactly starting material? and why it's small per cell?" nothing about CpG, therefore I did not include an answer about CpG. $\endgroup$ – user42909 Jun 7 '18 at 18:54

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