About

Genomics WA

 

Contact us on Genomics.WA@thekids.org.au for quotations for your projects or costings for your grants and for any urgent matters.

We look forward to helping you with your projects.

 

CHRISTMAS 2024 SHUTDOWN PERIOD

Our labs will be closed from 23 December 2024 to 6 January 2025 for Christmas. 
Our last day of Operations is Friday 20th December 2024.

Please submit your samples by 30 November 2024 if you wish to receive data before the Christmas break.

 

Overview of Services

Genomics WA is a genomics service provision laboratory in Perth, Australia. We provide cutting edge genomics and data analysis services to biomedical and non-biomedical researchers, our services are listed below.  Our laboratories are located on two sites on the QEII campus. Our DNA and RNA library preparation and Illumina sequencing laboratories are located on the 6th floor of the Perkins building and our Single cell Laboratory, long read sequencing laboratory and GWA TKI offices are located on the 6th and 7th floors of the Telethon Kids Institute.

For enquiries and quotations, contact us on Genomics.WA@telethonkids.org.au   OR use the Request a Quote tab.

 

 

 

Services on offer

Library preparation and sequencing

  1. RNA-Seq (polyA enrichment)
  2. Whole transcriptome RNA-Seq (ribodepletion)
  3. Whole transcriptome RNA-Seq for blood (ribo and globin depletion)
  4. Whole transcriptome RNA-Seq for plants (ribodepletion)
  5. Low input non stranded poly A RNA-Seq (SMARTSeq)
  6. Direct from cell RNA-seq (poly A, non stranded)
  7. Direct from cell BCR
  8. WGS with PCR (mechanical fragmentation)
  9. WGS with PCR (enzymatic fragmentation)
  10. WGS PCR free (transposase based)
  11. WGS PCR free (enzymatic fragmentation)
  12. WGS PCR free (Covaris Fragmentation)
  13. WGS for contaminated samples (Plant/Animal/microbial)
  14. WGS with UMIs for contaminated samples
  15. 16S sequencing for V3-V4 region
  16. Custom Amplicon Sequencing using primers provided by client
  17. ATAC-Seq
  18. ChIP-Seq
  19. EM-Seq
  20. Amplicon-Seq
  21. Whole Exome Sequencing
  22. Direct from cell WGS
  23. 3' end GEM-X from single cells on 10x Chromium
  24. 3' end GEM-X with feature barcoding on 10x Chromium
  25. 5' end GEM-X from single cells on 10x Chromium
  26. 5' GEM-X with V(D)J sequencing from single cells on 10x Chromium
  27. 5' GEM-X with V(D)J sequencing and feature barcoding from single cells on 10x Chromium
  28. 5' GEM-X with feature barcoding from single cells on 10x Chromium
  29. Single cell Multiome on 10x Chromium
  30. Single cell Flex (Fixed cell profiling) multiplexed or singleplexed on 10x Chromium 
  31. Single cell 3' or 5' GEM-X multiplexed with shallow WGS for deconvolution back to the original sample
  32. 16S library preparation for long read sequencing on Sequel II
  33. Library preparation for WGS (microbial) for long read sequencing on Sequel II
  34. Standard WGS library preparation for long read sequencing on Sequel II
  35. Longer WGS library preparation for long read sequencing on Sequel II
  36. Bespoke longer WGS library preparation for long read sequencing on Sequel II
  37. Custom Amplicon library preparation for long read sequencing on Sequel II
  38. Full length cDNA library preparation for long read sequencing on Sequel II
  39. MAS-Seq for single cell isoform profiling using  long read sequencing on Sequel II
  40. Spatial transcriptomics using Visium for Cyt Assist (Fresh frozen, Fixed frozen and FFPE archived slides)
  41. Spatial transcriptomics using Visium HD
  42. Spatial transcriptomics using Vizgen MERSCOPE

 

NGS services on the following sequencers

  1. NovaSeq6000
  2. MiniSeq
  3. MiSeq
  4. iSeq
  5. Pac Bio Sequel II

 

 

Bioinformatics data analysis services with set end points for libraries prepared and sequenced in our lab

1. For RNAseq: Analysis endpoint- Alignment and post alignment QC, Output is aligned files and post alignment QC 

2. For RNAseq: Analysis endpoint-List of DEGs and pathway analysis, Output is aligned files, post alignment QC, list of DEGs,  hierarchical clustering, PCA plots, basic pathway analysis and a report

3. For DNAseq: Analysis endpoint- Alignment and post alignment QC, Output is aligned files and post alignment QC 

4. For DNAseq: Analysis endpoint- List of raw variants

5. For 16S short read: Analysis endpoint - Dada2 output

6. For single cell workflows: Analysis endpoint: Cell Ranger analysis, Output is cell clusters called with lists of DEGs between clusters viewable on Loupe browser

7. For single cell workflows: Analysis endpoint: Seurat output

8. For Spatial transcriptomics on CytAssist: Analysis endpoint: Space ranger output

9. For VizGen Merscope spatial transcriptomics: Analysis endpoint: Cellpoze output

10. Bespoke analysis: Please discuss with us

 


Our laboratories are located at multiple sites on the QEII Campus. 

Sample submission is by appointment only, please see below locations for sample drop off based on service required

Drop off sample  Where Location
Cells for Single cell library preparation on Chromium 10x Single Cell Laboratory Room 633, Level 6 Telethon Kids Institute
Samples for MiniSeq sequencing MiniSeq Laboratory Room 633, Level 6 Telethon Kids Institute
Samples for long read library preparation and sequencing on Sequel II PacBio Sequel II Laboratory Room 756, Level 7 Telethon Kids Institute
Samples for library preparation from DNA, RNA, spatial transcriptomics Pre PCR laboratory Level 1 Perkins Building
Samples for Illumina Sequencing (except MiniSeq) Post PCR laboratory Level 1 Perkins Building

 

 

Equipment use Locations

Instrument Location
Tapestation 4200 HPIMR QC area, Level 6 Perkins Building
Qubit TKI Room 633, Level 6, Telethon Kids Institute
Qubit HPIMR QC area, Level 6 Perkins Building
Vacuum dryer Pre PCR, HPIMR  Pre-PCR laboratory, Level 1 Perkins Building
Vacuum dryer Post PCR, HPIMR  Post-PCR laboratory, Level 1 Perkins Building
Covaris E220 (coming soon) Pre-PCR laboratory, Level 1 Perkins Building
Tapestation 4200 TKI Room 633, Level 6 Telethon Kids Institute
Bioanalyser for DNA Room 633, Level 6 Telethon Kids Institute
Bioanalyser for RNA Room 633, Level 6 Telethon Kids Institute

 

Our team

 

Name Role Email
Prof. Alka Saxena Director alka.saxena@perkins.org.au
Dr. Hadi Shamaileh Technical manager Hadi.AlShamaileh@thekids.org.au
Dr Ulrich Kadolsky Bioinformatics and IT Manager ulrich.kadolsky@perkins.org.au
Dr Ali Sadiq Cheema Scientific Officer   Alisadiq.Cheema@thekids.org.au
Dr Xiao Zhong Bioinformatics Scientist  Xiao.Zhong@thekids.org.au
Dr Clementine Merce Bioinformatics Scientist  Clementine.Merce@thekids.org.au
Ms Reenu Joy Genomics Technician   Reenu.Joy@thekids.org.au
Mr Jefferson Allan  Bioinformatocs Scientist  Jefferson.Allan@thekids.org.au
Mr Paul Egan Quality Assurance Lead paul.egan@perkins.org.au
Ms Emma Tulloch Quality Assurance Officer emma.tulloch@perkins.org.au


Our Funding Partners
 

Genomics WA gratefully acknowledges funding received in cash and kind from all our funding partners.

Genomics WA is funded by a co-investment from BioPlatforms Australia, WA Department of Jobs, Tourism, Science and Innovation (JTSI), University of Western Australia, Harry Perkins Institute of Medical Research and Telethon Kids Institute as part of the NCRIS (National Collaborative Research Infrastructure Strategy) capability.

We are grateful for the support of the Perron Foundation and The Marshall Centre  for the donation of $1 million, which has enabled the purchase of the PacBio Sequel II, a long-read sequencing platform.

We gratefully acknowledge the support from the Australian Cancer Research Foundation for the Centre for Advanced Cancer Genomics which has made available the Illumina Novaseq6000 and Nanostring sprint systems for the use of Genomics WA.

 

Contacts

Name Role Phone Email Location
Alka Saxena
Director, Genomics WA
 
Phone +61 6151 0763 and +61 6319 1110
 
alka.saxena@perkins.org.au
 

 

Available Equipment and Resources

Name Price