Hi,
When running an NGS we get tens or hundreds of reads. These reads are calls of amplified DNA fragments of the patient. My question is, how many cells have provided the DNA fragments? When extracting DNA and creating a library, HOW MANY CELLS HAVE PROVIDED THE DNA? Any articles, references and your answers will be welcomed.
Tnx
•
written
by
erezts •
1 answer
It is easy to compute. You just need the ng of DNA input in the NGS experiment. For example, assume we input 250 ng of DNA (that is what is required in a standard WGS experiment*). Each cell contains 6 pg of DNA, hence, the number of cells is:
250 ng * (1000 pg / 1 ng) * (1 cell / 6 pg**) = 41,667.67 cells
*http://genomics.broadinstitute.org/products/whole-genome-sequencing
*The amount of 6 pg per cell can be estimated from: human genome is around 6200 Mbp, the average nucleotide molecular weight is about 660 g/bp mol and Avogadro's number is 6.022 10^23. Hence:
6200 Mbp * (10^6 bp/ 1 Mbp) * (1 bp mol/ 6.022 * 10^23 bp) * (660 g/ 1 bp mol) * (10^12 pg/ 1 g)= 6.795 pg
Of course, as stated by ATpoint in the comment, the amount of input DNA highly depends on the NGS experiment.
Log in to answer this question.
-
10x 3' library creates R1 and R2 fastq files with the same read length
written by tomas4482 •
-
Illumina technology output, 16S amplicon
written by Jelo •
-
SCRNA-seq experiment reads
written by kanwarjag
-
Questions from beginner: Barcode of Single cell RNA-seq
written by SDin •
-
FeatureCounts fails to count fragments instead of reads
written by Wietje
-
Understanding terms, specifically relating to GT:PL in a VCF file
written by rightmirem •
-
Capping the number of reads that align to a single k-mer
written by Morgan Ivy •
-
Next generation sequencing methodology
written by ansarruby22 •
-
Just need to learn to do one thing: counting the reads that map to the human mitochondrial genome
written by viottimanuel •
-
what are short reads in Chip Seq and how come there are so many?
written by Affan
This is not really bioinformatics so it likely will get closed. The answer is "it depends" and the dependency is the number of cells the wetlab used to extract DNA (or RNA, or whatever you measure). Can be millions, thousands, or in case of single-cell technology a single one. You will need to read the method sections of the paper to find which assay and kit was used, and then read the respective manual to get an idea.