Took the bisulfite-treated DNA from 20151218 and made Illumina libraries using the [TruSeq DNA Methylation Library Kit (Illumina)(https://github.com/sr320/LabDocs/blob/master/protocols/Commercial_Protocols/Illumina_truseq-dna-methylation-library-prep-guide-15066014-a.pdf).

Quantified the completed libraries using the Qubit 3.0 dsDNA BR Kit (ThermoFisher).

Evaluated the DNA with the Bioanalyzer 2100 (Agilent) using the DNA 12000 assay. Illumina recommended using the High Sensitivity assay, but we don’t have access to that so I figured I’d just give the DNA 12000 assay a go.

**SampleName**	**IndexNumber**	**BarCode**
1NF11	1	ATCACG
1NF15	2	CGATGT
1NF16	3	TTAGGC
1NF17	4	TGACCA
2NF5	5	ACAGTG
2NF6	6	GCCAAT
2NF7	7	CAGATC
2NF8	8	ACTTGA
M2	9	GATCAG
M3	10	TAGCTT
NF2_6	11	GGCTAC
NF_18	12	CTTGTA

Results:

Library Quantification (Google Sheet): 20151221_quantification_illumina_methylation_libraries

<td data-sheets-value="[null,2,"Test Name"]" >**Test Name** </td> <td data-sheets-value="[null,2,"Original sample conc."]" >**Concentration (ng/μL) ** </td> <td data-sheets-value="[null,2,"1NF11"]" >1NF11 </td> <td data-sheets-value="[null,2,"Out of range"]" >Out of range </td> <td data-sheets-value="[null,2,"1NF15"]" >1NF15 </td> <td data-sheets-value="[null,2,"1NF16"]" >1NF16 </td> <td data-sheets-value="[null,2,"1NF17"]" >1NF17 </td> <td data-sheets-value="[null,2,"2NF5"]" >2NF5 </td> <td data-sheets-value="[null,2,"2NF6"]" >2NF6 </td> <td data-sheets-value="[null,2,"Out of range"]" >Out of range </td> <td data-sheets-value="[null,2,"2NF7"]" >2NF7 </td> <td data-sheets-value="[null,2,"2NF8"]" >2NF8 </td> <td data-sheets-value="[null,2,"M2"]" >M2 </td> <td data-sheets-value="[null,2,"Out of range"]" >Out of range </td> <td data-sheets-value="[null,2,"M3"]" >M3 </td> <td data-sheets-value="[null,2,"NF2_6"]" >NF2_6 </td> <td data-sheets-value="[null,2,"NF2_18"]" >NF2_18 </td> <td data-sheets-value="[null,2,"Out of range"]" >Out of range </td>

2.14
2.74
2.64
2.92
2.42
2.56
2.1
2.38

I used the Qubit’s BR (broad range) kit because I wasn’t sure what concentrations to expect. I need to use the high sensitivity kit to get a better evaluation of all the samples’ concentrations.

Bioanalyzer Data File (Bioanalyzer 2100): 2100_20expert_DNA_2012000_DE72902486_2015-12-21_16-58-43.xad

(http://eagle.fish.washington.edu/Arabidopsis/20151221_bioanalyzer_illumina_methylation_libraries.jpg)

Ha! Well, looks like you definitely need to use the DNA High Sensitivty assay for the Bioanalyzer to pick up anything. Although, I guess you can see a slight hump in most of the samples at the appropriate sizes (~300bp); you just have to squint. ;)