UTSW Genomics Sequencing & Microarray Core Facility

Comprehensive coverage – Designed to interrogate all mature miRNA sequences in miRBase Release 20. Easily correlate miRNA results – Analysis files contain host gene ID, predicted and validated miRNA target genes, and clustered miRNA information.
Easy analysis – Analyze human, mouse, rat, or every miRNA for all species using the same array. Low sample input – Requires as little as 130 ng total RNA.
Simple, fast, and free analysis solution – Coupled with Affymetrix® Expression Console™ Software and Affymetrix® Transcriptome Analysis Console (TAC) Software, researchers have a complete solution from data to decision-making in minutes

Autoantigen array panel I contains 95 autoantigens and 8 internal control antigens, including nuclear antigens, cytoplasmic antigens, membrane antigen, phospholipid antigens, etc. The autoantigens are printed on 16-pad FAST slide. Each chip contains 16 identical arrays and can process 15 samples and one PBS control

A total of 5-10ng ChIP DNA is required. 

Accelerate your biomarker discovery with Clariom D solutions—the next generation of transcriptome-level profiling tools—providing a highly detailed view of the transcriptome for the fastest path to actionable results. Available for human, mouse, and rat, Clariom D solutions allow translational scientists to generate high-fidelity biomarker signatures quickly and easily with a design that provides the most intricate transcriptome-wide gene- and exon-level expression profiles including the ability to detect alternative splicing events of coding and long non-coding RNA, in a single three-day experiment.

Clariom S assays focus on well-annotated genes (>20,000), providing researchers with the ability to perform gene-level expression profiling studies and to quickly assess changes in key genes and pathways. With less time required for data analysis, Clariom S assays help researchers reach conclusions more rapidly.

Clariom S assays focus on well-annotated genes (>20,000), providing researchers with the ability to perform gene-level expression profiling studies and to quickly assess changes in key genes and pathways. With less time required for data analysis, Clariom S assays help researchers reach conclusions more rapidly.

Our core offers whole genome-seq library prep service for the following organisms.

• Mycobacterium tuberculosis (MTB)-4.0MB
• Staphylococcus aureus (SA)-2.8MB
• E. coli – 5.5MB
• Pseudomonas- 6MB
• Klebsiella pneumoniae- 5.3MB
• Homo sapiens 3234.83-MB

The service includes fragmentation, adding adaptors, size selection, amplification and QC.

 A minimum of 200ng DNA is required. We prefer to have 1 ug DNA. The DNA quality should be good. The volume is up to 35ul without EDTA. 

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

MiSeq V3 kit normally generates 20 to 25 million reads per flowcell.

MiSeq V3 kits normally generates 20 to 25 million reads per flowcell.

NextSeq 500/550 High Output Kit V2.5 normally generates about 400 million reads per flowcell. We prefer to order by FC.

NextSeq 500/550 High Output Kit V2.5 normally generates about 400 million reads per flowcell. We prefer to order by FC.

NextSeq 500/550 High Output Kit V2.5 normally generates about 400 million reads per flowcell. We prefer to order by FC.

Sequences are aligned with HISAT2 (Kim et al. 2015), duplicates are removed using Samtools (Li et al. 2009) and counts are generated using FeatureCount (Liao et al 2014). Transcript assembly and FPKM abundances are determined using StringTie (Pertea et al. 2015).  For Tumor samples, gene fusions can be detected using STAR-Fusion.

1. Kim D, Langmead B, Salzberg SL (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods. Apr;12(4):357-60. doi: 10.1038/nmeth.3317. Epub 2015 Mar 9. PubMed PMID: 25751142.
2. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009). The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9.PMID: 19505943.
3. Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.
4. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. PubMed PMID: 25690850.
5. Brian Haas, Alexander Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle, Asma Bankapur, Carrie Ganote, Thomas Doak, Natalie Pochet, Jing Sun, Catherine Wu, Thomas Gingeras, Aviv Regev. STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. bioRxiv 120295; doi: https://doi.org/10.1101/120295>;

PROCARTAPLEX 5 PLEX, 1PLATE 5-PLEX

Assay Id: MXCE4KT

Human analytes:

1. COMP (64)

2. IL-1 beta (18)

3. IL-10 (28)

4. LAP (29)

5. TNF alpha (45)

PROCARTAPLEX 2 PLEX, 1PLATE 2-PLEX

Assay ID is MXDJX6P

Human analytes

1. IL-6 (25)

2. MMP-1 (64)

We have the kits avaliable for the species: human, mouse, rat, bacteria, and host plus bacteria. For other species, please contact us.

Sample submision requirement: 100 ng to 2.5ug high-quality total RNA (RIN equal or above 7.0) in nuclease free H2O, and volume is up to 30ul. If the quantity is not a problem, we prefer to have 2.5 ug of total RNA.

If you have limited quantity, we have the low input kit avaliable for a minimum 25ng to start. But the species are limited to human, mouse and rat. The volume is up to 15ul.

mRNAseq-Strand specific library Preparation is primarily offered.

Please provide 100-2000ng good quality total RNA (RIN equal or above 7.0) in nuclease free H2O. The volume is up to 50ul. If you have limited quantity, the total RNA input can be lower to 50ng. But if the quantity is not a problem, we prefer to have 1-2 ug of total RNA.

We offer non strand mRNA library prep only if you need to compile with an old data set.

Please provide 1ug good quality total RNA including micro RNA (RIN equal or above 7.0) in 5 ul nuclease free H2O.

The price is per one time qPCR up to 10 samples.

Comprehensive coverage – Designed to interrogate all mature miRNA sequences in miRBase Release 20. Easily correlate miRNA results – Analysis files contain host gene ID, predicted and validated miRNA target genes, and clustered miRNA information.
Easy analysis – Analyze human, mouse, rat, or every miRNA for all species using the same array. Low sample input – Requires as little as 130 ng total RNA.
Simple, fast, and free analysis solution – Coupled with Affymetrix® Expression Console™ Software and Affymetrix® Transcriptome Analysis Console (TAC) Software, researchers have a complete solution from data to decision-making in minutes

Accelerate your biomarker discovery with Clariom D solutions—the next generation of transcriptome-level profiling tools—providing a highly detailed view of the transcriptome for the fastest path to actionable results. Available for human, mouse, and rat, Clariom D solutions allow translational scientists to generate high-fidelity biomarker signatures quickly and easily with a design that provides the most intricate transcriptome-wide gene- and exon-level expression profiles including the ability to detect alternative splicing events of coding and long non-coding RNA, in a single three-day experiment.

Clariom S assays focus on well-annotated genes (>20,000), providing researchers with the ability to perform gene-level expression profiling studies and to quickly assess changes in key genes and pathways. With less time required for data analysis, Clariom S assays help researchers reach conclusions more rapidly.

Clariom S assays focus on well-annotated genes (>20,000), providing researchers with the ability to perform gene-level expression profiling studies and to quickly assess changes in key genes and pathways. With less time required for data analysis, Clariom S assays help researchers reach conclusions more rapidly.

Autoantigen array panel I contains 95 autoantigens and 8 internal control antigens, including nuclear antigens, cytoplasmic antigens, membrane antigen, phospholipid antigens, etc. The autoantigens are printed on 16-pad FAST slide. Each chip contains 16 identical arrays and can process 15 samples and one PBS control

PROCARTAPLEX 5 PLEX, 1PLATE 5-PLEX

Assay Id: MXCE4KT

Human analytes:

1. COMP (64)

2. IL-1 beta (18)

3. IL-10 (28)

4. LAP (29)

5. TNF alpha (45)

PROCARTAPLEX 2 PLEX, 1PLATE 2-PLEX

Assay ID is MXDJX6P

Human analytes

1. IL-6 (25)

2. MMP-1 (64)

Sequences are aligned with HISAT2 (Kim et al. 2015), duplicates are removed using Samtools (Li et al. 2009) and counts are generated using FeatureCount (Liao et al 2014). Transcript assembly and FPKM abundances are determined using StringTie (Pertea et al. 2015).  For Tumor samples, gene fusions can be detected using STAR-Fusion.

1. Kim D, Langmead B, Salzberg SL (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods. Apr;12(4):357-60. doi: 10.1038/nmeth.3317. Epub 2015 Mar 9. PubMed PMID: 25751142.
2. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009). The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9.PMID: 19505943.
3. Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.
4. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. PubMed PMID: 25690850.
5. Brian Haas, Alexander Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle, Asma Bankapur, Carrie Ganote, Thomas Doak, Natalie Pochet, Jing Sun, Catherine Wu, Thomas Gingeras, Aviv Regev. STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. bioRxiv 120295; doi: https://doi.org/10.1101/120295>;

A total of 5-10ng ChIP DNA is required. 

Our core offers whole genome-seq library prep service for the following organisms.

• Mycobacterium tuberculosis (MTB)-4.0MB
• Staphylococcus aureus (SA)-2.8MB
• E. coli – 5.5MB
• Pseudomonas- 6MB
• Klebsiella pneumoniae- 5.3MB
• Homo sapiens 3234.83-MB

The service includes fragmentation, adding adaptors, size selection, amplification and QC.

 A minimum of 200ng DNA is required. We prefer to have 1 ug DNA. The DNA quality should be good. The volume is up to 35ul without EDTA. 

Please provide 1ug good quality total RNA including micro RNA (RIN equal or above 7.0) in 5 ul nuclease free H2O.

mRNAseq-Strand specific library Preparation is primarily offered.

Please provide 100-2000ng good quality total RNA (RIN equal or above 7.0) in nuclease free H2O. The volume is up to 50ul. If you have limited quantity, the total RNA input can be lower to 50ng. But if the quantity is not a problem, we prefer to have 1-2 ug of total RNA.

We offer non strand mRNA library prep only if you need to compile with an old data set.

We have the kits avaliable for the species: human, mouse, rat, bacteria, and host plus bacteria. For other species, please contact us.

Sample submision requirement: 100 ng to 2.5ug high-quality total RNA (RIN equal or above 7.0) in nuclease free H2O, and volume is up to 30ul. If the quantity is not a problem, we prefer to have 2.5 ug of total RNA.

If you have limited quantity, we have the low input kit avaliable for a minimum 25ng to start. But the species are limited to human, mouse and rat. The volume is up to 15ul.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

Hiseq 4000 sequencer normally can generate 300 million reads per lane. Only 8 lanes flowcell is available. If you don't need 8 lanes at a time, you need to share the FC with others.

Please note there are some specific requirements for libraries in order to run Hiseq 4000 sequencer:

1) The library quality check by bioanalyzer is required.

MiSeq V3 kit normally generates 20 to 25 million reads per flowcell.

MiSeq V3 kits normally generates 20 to 25 million reads per flowcell.

NextSeq 500/550 High Output Kit V2.5 normally generates about 400 million reads per flowcell. We prefer to order by FC.

NextSeq 500/550 High Output Kit V2.5 normally generates about 400 million reads per flowcell. We prefer to order by FC.

NextSeq 500/550 High Output Kit V2.5 normally generates about 400 million reads per flowcell. We prefer to order by FC.

The price is per one time qPCR up to 10 samples.