UTSW Genomics Sequencing Core

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. 

• HLA-SLE_V5 custom target array-This array capture genetic variants across entire HLA region (Class I & II) and other Systemic Lupus Erythematosus (SLE) associated genes (more than 100 genes). Total design size is 7MB capture target.
• The package includes DNA library prep, target enrichment, and sequencing. 

Retrieve and transfer data from our backup server

 Any order less than 6 samples, a waiting period may apply. For a rush order, a minimum number of 6 samples per order is required. 

RRBS-seq (Reduced Representation Bisulfite Sequencing). The price includes RRBS-seq library preparation and sequencing. 

 Any order less than 6 samples, a waiting period may apply. For a rush order, a minimum number of 6 samples per order is required. 

Alignmentments will be generated using BWA-MEM used reference genome: (i) Mouse (GRCm38), (ii) Human (GRCh37, GRCh38), (iii) Rat (Rnor6.0) with subsequent processing by Samtools and Picard to ensure proper file formatting and mark duplicates. Germline variants are detected with (i) Strelka2, (ii) Platypus, (iii) Samtools and (iv) Speedseq.  Somatic variants are detected in cancer samples with a matched normal tissue pair with Mutect2, Speedseq, Shimmer, Varscan2, and Virmid.  Effect of SNPs and INDELs on genes was predicted using snpEff.  For human samples, general population allele frequency is determined by the GnomAD database.  For tumor samples run using the tumor gene panel protocol, CNVs are detected using CNVKit.

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. 

 Using picogreen and Nanodrop method to quantify samples' concentration. The minimum volume should be no less than 3 microliters!

The price includes the DNA library prep, the target enrichment, and the quality check for the final library.

• The SeqCap EZ Exome Kit v3.0 product covers more than 20,000 genes in the human genome. All the genome coordinates are based on human genome build GRCh37 (hg19). More than two million oligonucleotide DNA probes capture the target regions. Because the flanking regions of some coding exons and miRNAs are also covered by probes, the total size of the regions covered by probes is 64 Mb.

• The SeqCap EZ MedExome Kit is a new exome solution that queries the entire human exome with enhanced coverage for exons of disease-associated gene regions. The design targets the genome assembly GRCh38/hg38 (coordinates for hg19 annotation are also available) with comprehensive sequencing coverage of medically-relevant regions and protein coding regions. The product has been extensively optimized in design, empirical rebalancing, and manufacturing to increase coverage in hard-to-sequence regions for a more uniform and complete exome.This kit capture entire human exome with enhanced coverage for exons of disease-associated gene regions or medically relevant loci. Total design size is 47Mb capture target.

• MedExome + 1385 TruSight RNA Pan-Cancer Panel: MedExome content plus targeting 1385 cancer genes for gene expression, variant, and fusion detection studies in many RNA sample types including blood, bone marrow, and FFPE.

• MedExome + 1385 TruSight RNA Pan-Cancer Panel + HLA:MedExome content plus targeting 1385 cancer genes for gene expression, variant, and fusion detection studies in many RNA sample types including blood, bone marrow, and FFPE. It also has about 3MB region of HLA which captures exons as well as regulatory regions.

• MedExome PLUS- In the SeqCap EZ MedExome PLUS configuration, the product offers the ability to add up to 200 Mb of user-defined custom regions to the existing Medexome design.

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

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

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

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.

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.

Our core provides SARS-CoV-2 genome sequencing service using ARTICv3. (IDT) primers. We have optimized and validated our protocol on RT-PCR positive nasopharyngeal swab specimens from COVID-19 patient. Our assay provides 500K-1Million quality pass reads per genome for robust phylogenetic analysis. Our team also help with data analysis, if needed.

20 samples per batch is preferred.

about 2.5 billion reads per lane 

about 400 million reads per lane

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

The price is per sample
 *   Normalization
 *   Differential Gene expression analysis  and heat map
 

The price is per sample

Includes:

NextSeq 550 flowcell with PE-75 sequencing

Reagents

Picogreen

Kappa

Bioanalyzer

The package includes stranded mRNA library prep and SE-75 sequencing. The average reads per sample is about 30 million.

Customer needs to submit samples by N X of 12 samples per batch at a time.

The price includes DNA library prep, target enrichment, and PE- sequencing at an average ~ 100 X coverage

We have the kits avaliable for the species: human, mouse, rat. 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.

Require to submit a minimum of 10 RNA samples per order

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

Our core provides SARS-CoV-2 genome sequencing service using ARTICv3. (IDT) primers. We have optimized and validated our protocol on RT-PCR positive nasopharyngeal swab specimens from COVID-19 patient. Our assay provides 500K-1Million quality pass reads per genome for robust phylogenetic analysis. Our team also help with data analysis, if needed.

20 samples per batch is preferred.

Retrieve and transfer data from our backup server

Alignmentments will be generated using BWA-MEM used reference genome: (i) Mouse (GRCm38), (ii) Human (GRCh37, GRCh38), (iii) Rat (Rnor6.0) with subsequent processing by Samtools and Picard to ensure proper file formatting and mark duplicates. Germline variants are detected with (i) Strelka2, (ii) Platypus, (iii) Samtools and (iv) Speedseq.  Somatic variants are detected in cancer samples with a matched normal tissue pair with Mutect2, Speedseq, Shimmer, Varscan2, and Virmid.  Effect of SNPs and INDELs on genes was predicted using snpEff.  For human samples, general population allele frequency is determined by the GnomAD database.  For tumor samples run using the tumor gene panel protocol, CNVs are detected using CNVKit.

The price is per sample
 *   Normalization
 *   Differential Gene expression analysis  and heat map
 

The price is per sample

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. 

The price includes the DNA library prep, the target enrichment, and the quality check for the final library.

• The SeqCap EZ Exome Kit v3.0 product covers more than 20,000 genes in the human genome. All the genome coordinates are based on human genome build GRCh37 (hg19). More than two million oligonucleotide DNA probes capture the target regions. Because the flanking regions of some coding exons and miRNAs are also covered by probes, the total size of the regions covered by probes is 64 Mb.

• The SeqCap EZ MedExome Kit is a new exome solution that queries the entire human exome with enhanced coverage for exons of disease-associated gene regions. The design targets the genome assembly GRCh38/hg38 (coordinates for hg19 annotation are also available) with comprehensive sequencing coverage of medically-relevant regions and protein coding regions. The product has been extensively optimized in design, empirical rebalancing, and manufacturing to increase coverage in hard-to-sequence regions for a more uniform and complete exome.This kit capture entire human exome with enhanced coverage for exons of disease-associated gene regions or medically relevant loci. Total design size is 47Mb capture target.

• MedExome + 1385 TruSight RNA Pan-Cancer Panel: MedExome content plus targeting 1385 cancer genes for gene expression, variant, and fusion detection studies in many RNA sample types including blood, bone marrow, and FFPE.

• MedExome + 1385 TruSight RNA Pan-Cancer Panel + HLA:MedExome content plus targeting 1385 cancer genes for gene expression, variant, and fusion detection studies in many RNA sample types including blood, bone marrow, and FFPE. It also has about 3MB region of HLA which captures exons as well as regulatory regions.

• MedExome PLUS- In the SeqCap EZ MedExome PLUS configuration, the product offers the ability to add up to 200 Mb of user-defined custom regions to the existing Medexome design.

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.

Includes:

NextSeq 550 flowcell with PE-75 sequencing

Reagents

Picogreen

Kappa

Bioanalyzer

We have the kits avaliable for the species: human, mouse, rat. 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.

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.

about 2.5 billion reads per lane 

about 400 million reads per lane

• HLA-SLE_V5 custom target array-This array capture genetic variants across entire HLA region (Class I & II) and other Systemic Lupus Erythematosus (SLE) associated genes (more than 100 genes). Total design size is 7MB capture target.
• The package includes DNA library prep, target enrichment, and sequencing. 

RRBS-seq (Reduced Representation Bisulfite Sequencing). The price includes RRBS-seq library preparation and sequencing. 

The package includes stranded mRNA library prep and SE-75 sequencing. The average reads per sample is about 30 million.

Customer needs to submit samples by N X of 12 samples per batch at a time.

The price includes DNA library prep, target enrichment, and PE- sequencing at an average ~ 100 X coverage

Require to submit a minimum of 10 RNA samples per order

 Any order less than 6 samples, a waiting period may apply. For a rush order, a minimum number of 6 samples per order is required. 

 Any order less than 6 samples, a waiting period may apply. For a rush order, a minimum number of 6 samples per order is required. 

 Using picogreen and Nanodrop method to quantify samples' concentration. The minimum volume should be no less than 3 microliters!

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