Kun:LabNotes/HiResChrPaint: Difference between revisions

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===Overview===
===Overview===
===Barcode design===
===Barcode design===
*Each barcode has N number of digits, each digit can have M colors. We start with N=7 and M=4.
*To better resolve the barcodes, we require that two adjacent digits have different color. Therefore, the total number of possible barcodes is M*(M-1)^(N-1), which is 8748 when N=7 and M=4.
*The size of a digit depends on how well we can resolve a feature optically. Based on existing publications, this could be anywhere between 10-400kb.
*There could be a spacer between digits, but not necessary as long as two adjacent digits have different colors.
*We do need a spacer between two adjacent barcodes in order to know where the first digit is. As a start, the spacer can be twice as large as a digit.
*Here is an estimation of number of barcodes and probes needed for the entire human genome.
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Digit Size'''
| align="center" style="background:#f0f0f0;"|'''# probes/digit'''
| align="center" style="background:#f0f0f0;"|'''Digits/barcode'''
| align="center" style="background:#f0f0f0;"|'''# barcodes'''
| align="center" style="background:#f0f0f0;"|'''Barcode size'''
| align="center" style="background:#f0f0f0;"|'''Total region covered'''
| align="center" style="background:#f0f0f0;"|'''# probes needed for human genome'''
|-
| 50,000||400||5||324||350,000||113,400,000||648,000
|-
| || ||6||972||400,000||388,800,000||2,332,800
|-
| || ||7||2916||450,000||1,312,200,000||8,164,800
|-
| || ||8||8748||500,000||4,374,000,000||18,560,000
|-
| || || || || || ||
|-
| 100,000||400||5||324||700,000||226,800,000||648,000
|-
| || ||6||972||800,000||777,600,000||2,332,800
|-
| || ||7||2916||900,000||2,624,400,000||8,164,800
|-
| || ||8||8748||1,000,000||8,748,000,000||9,280,000
|-
| || || || || || ||
|-
| 200,000||400||5||324||1,400,000||453,600,000||648,000
|-
| || ||6||972||1,600,000||1,555,200,000||2,332,800
|-
| || ||7||2916||1,800,000||5,248,800,000||4,511,111
|-
| || ||8||8748||2,000,000||17,496,000,000||4,640,000
|-
|
|}
===Probe design===
===Probe design===
===Probe synthesis and labeling===
===Probe synthesis and labeling===

Revision as of 07:12, 17 February 2012

Project threads

Overview

Barcode design

  • Each barcode has N number of digits, each digit can have M colors. We start with N=7 and M=4.
  • To better resolve the barcodes, we require that two adjacent digits have different color. Therefore, the total number of possible barcodes is M*(M-1)^(N-1), which is 8748 when N=7 and M=4.
  • The size of a digit depends on how well we can resolve a feature optically. Based on existing publications, this could be anywhere between 10-400kb.
  • There could be a spacer between digits, but not necessary as long as two adjacent digits have different colors.
  • We do need a spacer between two adjacent barcodes in order to know where the first digit is. As a start, the spacer can be twice as large as a digit.
  • Here is an estimation of number of barcodes and probes needed for the entire human genome.
Digit Size # probes/digit Digits/barcode # barcodes Barcode size Total region covered # probes needed for human genome
50,000 400 5 324 350,000 113,400,000 648,000
6 972 400,000 388,800,000 2,332,800
7 2916 450,000 1,312,200,000 8,164,800
8 8748 500,000 4,374,000,000 18,560,000
100,000 400 5 324 700,000 226,800,000 648,000
6 972 800,000 777,600,000 2,332,800
7 2916 900,000 2,624,400,000 8,164,800
8 8748 1,000,000 8,748,000,000 9,280,000
200,000 400 5 324 1,400,000 453,600,000 648,000
6 972 1,600,000 1,555,200,000 2,332,800
7 2916 1,800,000 5,248,800,000 4,511,111
8 8748 2,000,000 17,496,000,000 4,640,000

Probe design

Probe synthesis and labeling

Hybridization and imaging

Image analysis

Daily Notes

2012 <calendar> name=Kun:LabNotes/HiResChrPaint format=%name/%year-%month-%day date=2012/02/01 view=oneyear </calendar>