Banana Slug Genomics

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
===== illumina Sequencing Run 1 =====
==== Meta ====
Prepared by Akram Tariq Sial

Date: 

Overview: This sample was prepared according to manufacturer's recommendations. [Add link to illumina protocol]

==== Starting DNA ====

==== Initial Size Selection ====

{{:lab_protocols:bana_slug_library_illumina.jpg?600}}
{{:lab_protocols:bana_slug_library_illumina._after_cutjpg.jpg.jpg?600}}

[[http://www.fermentas.com/en/products/all/dna-electrophoresis/generuler-dna-ladders/sm0373-generuler-50bp|Fermentas O'generuler 50bp ladder used in these gels.]] Lanes 1 & 6

1µg of 98.0 ng/µl genomic DNA was sheared using either Covaris or a Nebulizer. 
Lanes 3&4: Banana Slug DNA sheared using Covaris. 
Lanes 5&6: Banana Slug DNA sheared using a Nebulizer. Both were cut between 250-375 basepairs.

==== Bioanalyzer results of initial shearing and final amplified library size selection ====
{{:lab_protocols:bioanalyzer-illumina-library.pdf|Bioanalyzer results of shearing distributions and final amplified libraries.}} Covaris and Nebulizer shearing are in lanes 1 and 2 respectively. Amplified and size selected libraries for Nebulizer and Covaris in lanes 3 and 4 respectively. 

The results indicate the final nebulizer library ranges from 202-320bp in distribution. The final covaris library ranges from 225-263bp in length.

==== Final distribution of paired end reads ====
Each stage indicates a different distribution in the length of the paired-end reads.
The original size selection cut indicates a fragment size of 250-375. However, the bioanalyzer results indicate the final size selected fragment is much shorter at 200-320 bp for a final distribution between 100-230 bp.

==== Differences between lanes in illumina run ====
Each lane contained a different concentration of starting material used in bridge amplification.
^Lane ^ Starting amount of library and library type ^
|Lane 1 | 8 picoMoles Nebulized Library |
|Lane 2 | 10 picoMoles Nebulized Library |
|Lane 3 | 12 picoMoles Nebulized Library |
|Lane 4 | 6 picoMoles phix control* |
|Lane 5 | 8 picoMoles Covaris Library |
|Lane 6 | 10 picoMoles Covaris Library |
|Lane 7 | 12 picoMoles Covaris Library |
|Lane 8 | 14 picoMoles Covaris Library |

These different starting quantities of DNA are reflected in the number of clusters generated and the total reads outputted for each lane. Additionally, a different distribution of distance for the paired-end reads are different for lanes 1-3 and 5-8

*Data from lane 4 of the illumina run **SHOULD NOT** be used for assembly
Banana Slug Genomics

User Tools

Site Tools

Page Tools
