Bioplatforms Australia Datasets Initiative
IlluminaHiSeq 2000 Sample submission form
ResearcherContact Details
Email:
Phone:
diana.garnica@anu.edu.au
61-02-61256963
Address:
Linnaeus building # 134, room 3.077. The Australian National University,
Acton 0200, ACT.
Name:Diana Garnica and John Rathjen
Institution / Organisation:
The Australian National University
Sample Information
Organism / Species
Sample type
DNA/RNA
Part of organism RNA/RNA extracted from
Extraction method
Comments / special considerations
Pucciniastriiformisf.sptritici (Pst) and Triticumaestivum(Ta)
RNA
From Pst, ungerminated spores, from Ta healthy and infected leaves
RNAeasy Plant kit QIAGEN
Growth protocol of fungus and/or plant (medium, soil, water regimen, light/day, fertilisers etc):
Wheat seedling were grown at 21C for two weeks, then infected with fungal spores and maintained in a wet chamber at 9C for 48h. Subsequently plants
were moved to a growth chamber at 17C in 16/8 light cycle. Collection of infected tissue was done a different time points during the process mentioned
above. Healthy tissue was collected from uninfected plants. Germinated spores were collected ~17 days after infection when the plant tissue is fully
covered in spores.
BPA Project: Ramaciotti Sequencing submission form
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Treatment protocol (i.e. route of administration of pathogen):
Ungerminated spores of the pathogen are mixed with talk and sprayed onto wet wheat seedlings.
Further Information on experimental design (i.e. timepoints and biological replicates):
Three biological replicates from different time points along the infection were collected and sequenced (0 hai and6 dai). Only one sample 9 dai was
collected s in the past we had sequenced two replicates. Also, three replicates of ungerminated spores were sequenced. Finally, one replicate of wheat
leave tissue infiltrated with buffer and one replicate of wheat leave tissue infiltrated with spores extract were sequenced.
BPA Project: Ramaciotti Sequencing submission form
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Sample Name
Volume
(ul)
RIN
(RNA)
OD
260/280
OD
260/230
Conc.(ng/ul)
Additional Information.
(method used)
Sample 1
DG1
50 ul
>8.0
>200 ng/ul
Unger-spores r1
Sample 2
DG2
50 ul
>8.0
>200 ng/ul
Unger-spores r2
Sample 3
DG3
50 ul
>8.0
>200 ng/ul
Unger-spores r3
Sample 4
DG4
50 ul
>8.0
>200 ng/ul
Infected tissue 0 hai r1
Sample 5
DG5
50 ul
>8.0
>200 ng/ul
Infected tissue 0 hai r2
Sample 6
DG6
50 ul
>8.0
>200 ng/ul
Infected tissue 0 hai r3
Sample 7
DG7
50 ul
>8.0
>200 ng/ul
Infected tissue6 dai r1
Sample 8
DG8
50 ul
>8.0
>200 ng/ul
Infected tissue6 dai r2
Sample 9
DG9
50 ul
>8.0
>200 ng/ul
Infected tissue6 dai r3
Sample 10
DG10
50 ul
>8.0
>200 ng/ul
Infected tissue9dai
Sample 11
DG11
50 ul
>8.0
>200 ng/ul
Wheat infiltrated with buffer
Sample 12
DG12
50 ul
>8.0
>200 ng/ul
Wheat infiltrated with spores extract
Attach additional sheet if more samples
BPA Project: Ramaciotti Sequencing submission form
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Sample Requirements
RNA
•
•
•
Samples should be intact and not degraded as assessed by a Bioanalyzer. The RNA Integrity Number (RIN) value should be greater than 8.
OD 260/280 ratio of 2, and a 260/230 of 1.8-2.
5 μg of total RNA at min concentration of 200ng/ul (optimal 500ng/ul). The concentration should be measured using the Ribogreen
fluorescent assay.
Samples should be resuspended in nuclease-free water or elution buffer.
RNA that has been extracted using Trizol or any phenol based method must undergo an additional column purification
•
•
Sample shipment details

Samples to be shipped on dry ice.
Facility
The Ramaciotti Centre
Address
Lowy Cancer Research Centre
C25
via Gate 11 Botany Street
University of New South Wales
Randwick, NSW 2052
Contact person
Tonia Russell
Phone: (02) 93851658
Email: illumina@unsw.edu.au
Please email a copy of the completed form to Anna Fitzgerald (afitzgerald@bioplatforms.com) at the time of sample submission and complete Google Docs metadata form.
BPA Project: Ramaciotti Sequencing submission form
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