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We aim to have a cell-type specific eQTL study (ct-eQTL) for B cells with available budget $35,000. As the optimal coverage at an average sequencing cost of 5$ per 1 million reads is 10,000 reads per cell (Mandric et al, 2019), what is the sample size and the number of cells we should have per individual? And what will be the effective sample size?
Cell type CD4 T cells CD14+ Monocytes B cells CD8 T cells NK cells FCGR3A+ cells Megakaryocytes Dendritic cells	Budget ($1,000)	Sequencing cost (per 1M reads) 1 $ 2 $ 3 $ 4 $ 5 $

Calculating results

Main assumptions This calculator provides guidance in selecting optimal experimental designs for cell-type specific eQTL analysis (ct-eQTL). It is based on the results of the paper "Optimal design of single-cell RNA sequencing experiments for cell-type specific eQTL analysis" (Mandric et al, 2019). As it is shown in their paper, the optimal coverage at which one should conduct cell-type specific eQTL studies is 10,000 (±2,500) reads per cell. The assumptions underlying this calculator are the following: Genetic multiplexing is used At most 16 samples per pool At most 24,000 cells per pool The cost of library prep is $2,000 per reaction The cost of sequencing is $5 per million reads How to interpret the output of the calculator? The area of best experimental designs is marked with a blue dashed line The Optimal Effective Sample Size is the same for all the experimental designs inside the marked area The blue dots show some particular experimental designs. Hover the mouse upon them to see the number of pools and number of reads per cell The number of cells stands for desired number of cells This calculator was developed by Igor Mandric (UCLA) and Christoph Hafemeister (NYGC).