Infos to lab Users

ACDB’S LABORATORY RULES RELATED TO SEQUENCING


1. DNA Extraction:

All DNA extractions (using the CTAB method only) must be listed in an Excel extraction sheet and send to Salome (salomalgas@gmail.com) and Olivier (olive.maurin@gmail.com) electronically. A template form is available here (Download).

The Extraction sheet should contain the following information:

a. Full Name of person extracting

b. Date of extraction

c. Voucher name

d. Taxon name

e. Weight of plant material extracted

f. Method of precipitation (Ethanol / Isopropanol)

g. A gel picture of all DNA extract from 10 ul before precipitation

 

Note 1: The voucher name used must be agreed with Olivier in order to gain uniformity in the UJ-ACDB DNA bank. This will also simplify the submission of sequences and trace files to GenBank and BOLD)

Note 2: All sequences generated at the ACDB should be submitted to GenBank, via the www.boldsystems.org.

 

2. DNA Sequencing:

When preparing your cycle sequencing sheet you need to follow the guidelines listed below and send it electronically to Ronny (ronnym@uj.ac.za) copied to Olivier (olive.maurin@gmail.com):

a. Enter your name, number of reactions and regions sequenced in the Sequencing book located in the lab.

b. Prepare your sequencing sheet as required by Ronny. A template form is available here (Download).

c. The format of your sequences name must be standardised as: d. Voucher Name_PrimerNameDirection

i. Voucher name as in 1c (exact same spelling)

ii. A list of most PrimerNameDirection is listed here (Download). If the primers you are using are not listed contact Olivier.

 

3. Managing of Sequences in User Account:

In your user account on the computer, data must be organised in folders as follow:

a. “1.Incoming Sequences”

b. “2.Sequences”

c. “3.Matrix”

 

When receiving sequences from Ronny via Drop Box, transfer sequences into the “1. Incoming folder” in your user account.

Before proceeding with editing, organise all  .ab1 files and .phd1 files within “2.Sequences” as follows:

Create one folder for each genes/regions  sequenced (e.g. ITS, trnL-F, and/or atpB-rbcL)

Note 3: If you have used internal primers all sequences have to be located within the same gene folder (e.g. ITS-101-F, ITS-2-R, ITS-3-F and ITS-102-R should be included within the ITS folder)

Within each gene/regions folders, organise your sequences as follows:

>Genus name

>Genus initial. Species name_Voucher

After editing your sequences using “Sequencher”, save the project using the following standard: Voucher_gene (e.g. OM2304_trnH-psbA).

A backup of your project should be provided on submission of your dissertation/thesis to Olivier (olive.maurin@gmail.com).

 

Note 4: If you have any questions regarding any of the above, please contact Olivier.


Note 5: Not complying with the above will delay your own work, as your data will not be accepted in any other format.


Olivier Maurin

olive.maurin@gmail.com

05 May 2014