1363983501859 145375dfb8ed1b7723376b467bd3f18f

UR Genomics Research Center

Rochester, New York, US

The GRC (grc-srl.urmc.edu) is a core resource that supports all aspects of genomics research at the University of Rochester and to external US academic institutions.

Instrumentation: Illumina Hiseq2500v4, 2 Illumina Miseqs, Fluidigm C1, 10X Genomics Chromium Controller, Agilent Bioanalyzers, Agilent TapeStation, QuantStudio 12k Flex qPCR system with OpenArray capability, Covaris S2 system, QX100 digital droplet PCR system, Pippin Prep, Eppendorf EpMotion 5070 and 5075 liquid handling systems, and various thermocyclers.

RNA Sequencing:
Standard sample requirements: If providing tissue or cells, we require enough material to obtain at least 0.2 - 0.5ug of total RNA. For purified RNA, we recommed submiting at least 0.2ug of purified total RNA in ultra pure water. DNase treatment of RNA is necessary and can be done prior to submission using Turbo DNase or the GRC will perform this for a fee. Sample quantity and... Show more »

The GRC (grc-srl.urmc.edu) is a core resource that supports all aspects of genomics research at the University of Rochester and to external US academic institutions.

Instrumentation: Illumina Hiseq2500v4, 2 Illumina Miseqs, Fluidigm C1, 10X Genomics Chromium Controller, Agilent Bioanalyzers, Agilent TapeStation, QuantStudio 12k Flex qPCR system with OpenArray capability, Covaris S2 system, QX100 digital droplet PCR system, Pippin Prep, Eppendorf EpMotion 5070 and 5075 liquid handling systems, and various thermocyclers.

RNA Sequencing:
Standard sample requirements: If providing tissue or cells, we require enough material to obtain at least 0.2 - 0.5ug of total RNA. For purified RNA, we recommed submiting at least 0.2ug of purified total RNA in ultra pure water. DNase treatment of RNA is necessary and can be done prior to submission using Turbo DNase or the GRC will perform this for a fee. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and the Agilent Bioanalyzer 2100 profile. RIN (RNA Integrity Number) values of >7.0 and OD260/280 = 2.0 - 2..2 are recommended for RNA-seq library preparation. For samples with low RNA abundance, there are alterantive methods that can be used for RNA inputs of 1ng and below.

Small RNA Sequencing
If providing tissue or cells, we require enough material to obtain at least 1-2ug of total RNA. For purified RNA, we recommed submiting at least 1-2ug of purified total RNA or enriched small RNA from 1-2ug total RNA (~50ng) in ultra pure water. DNase treatment of RNA is necessary and can be done prior to submission using Turbo DNase or the GRC will perform this for a fee. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and the Agilent Bioanalyzer 2100 profile.

DNA Sequencing:
If providing tissue, blood or cells, we require enough material to obtain at least 2ug of total gDNA. For purified gDNA, we recommed submiting at least 2ug of purified total gDNA in ultra pure water. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and the Agilent Bioanalyzer 2100 profile. We recommend DNA purity with an OD260/280=1.8-2.0 without degradation or RNA contamination.

ChIP Sequencing:
Please submit at least 20-50ng of ChIP or capture kit enriched DNA in ultra pure water. We strongly recommend verification of the ChIP samples with qPCR prior to submission for ChIP-seq library contruction. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and the Agilent Bioanalyzer 2100 profile. We recommend DNA purity with an OD260/280=1.8-2.0 without RNA contamination and a size profile os 200-500bp.

Standard deliverables:

Raw FASTQ files
Quality filtered FASTQ files
Alignment files
FASTQC quality metrics for each sample sequenced
FPKM normalized differential gene expression results
Gene counts
Differentially expressed genes filtered for significance (CI>95%)
Readme file describing the process

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UR Genomics Research Center has not listed any services.

DNA Sequencing Data Analysis
Price on request
Request a quote for more information about this service.
ATAC-Seq
Assay for Transposase-Accessible Chromatin with High Throughput Sequencing
Starting at $120.00 per sample

We require a consultation prior to performing or quote for ATAC-seq projects.

We require a consultation prior to performing or quote for ATAC-seq projects.

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Single Cell RNA-Seq
Price on request

Fluidigm C1 or 10X genomics platform

Highly viable cells required for capture. Fluidigm C1 is capable of capturing up to ~800 single cells and 10X genomics up to ~50,000 cells. Price includes basic data processing. Additional analyses available.

Fluidigm C1 or 10X genomics platform

Highly viable cells required for capture. Fluidigm C1 is capable of capturing up to ~800 single cells and 10X genomics up to ~50,000 cells. Price includes basic data processing. Additional analyses available.

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Low Input/Single Cell RNA Sequencing
Starting at $315.00 per sample

Standard sample requirements:

If providing tissue or cells, we require enough material to obtain at least 5-10ng of total RNA. For purified RNA, we recommed submiting at least 10ng of purified total RNA in ultra pure water. Sample quantity and quality will be verified with fluorometry (Qubit) and the Agilent Bioanalyzer 2100... Show more »

Standard sample requirements:

If providing tissue or cells, we require enough material to obtain at least 5-10ng of total RNA. For purified RNA, we recommed submiting at least 10ng of purified total RNA in ultra pure water. Sample quantity and quality will be verified with fluorometry (Qubit) and the Agilent Bioanalyzer 2100 profile. RIN (RNA Integrity Number) values of >7.0 and OD260/280 = 2.0 - 2.2 are recommended for RNA-seq library preparation.

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Illumina HiSeq 2500 sequencing system
QuantStudio 12K Flex
Whole Genome Bisulfite Sequencing
Starting at $384.00 per sample

Sample requirements:
If providing tissue, blood or cells, we require enough material to obtain at least 1ug of total gDNA. For purified gDNA, we recommed submiting at least 1ug of purified total gDNA in ultra pure water. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and... Show more »

Sample requirements:
If providing tissue, blood or cells, we require enough material to obtain at least 1ug of total gDNA. For purified gDNA, we recommed submiting at least 1ug of purified total gDNA in ultra pure water. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and gel electropheresis. We recommend DNA purity with an OD260/280=1.8-2.0 without degradation or RNA contamination.

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QuantStudio 12K Flex
Truseq RNA Library Preparation
Starting at $250.00 per sample

TruSeq RNA v2 $250.00
TruSeq Stranded mRNA-seq $250.00
TruSeq Total stranded RNA-seq $350.00
(Human, Mouse, Rat)
TruSeq Small RNA-seq $350.00
TruSeq DNA-seq (nano kit) $284.00
TruSeq PCR Free DNA ... Show more »

TruSeq RNA v2 $250.00
TruSeq Stranded mRNA-seq $250.00
TruSeq Total stranded RNA-seq $350.00
(Human, Mouse, Rat)
TruSeq Small RNA-seq $350.00
TruSeq DNA-seq (nano kit) $284.00
TruSeq PCR Free DNA $294.00

Standard sample requirements:

If providing tissue or cells, we require enough material to obtain at least 0.2 - 0.5ug of total RNA. For purified RNA, we recommed submiting at least 0.2ug of purified total RNA in ultra pure water. DNase treatment of RNA is necessary and can be done prior to submission using Turbo DNase or the GRC will perform this for a fee. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and the Agilent Bioanalyzer 2100 profile. RIN (RNA Integrity Number) values of >7.0 and OD260/280 = 2.0 - 2.2 are recommended for RNA-seq library preparation. For samples with low RNA abundance, there are alterantive methods that can be used for RNA inputs of 1ng and below.

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QuantStudio 12K Flex
Whole Exome Sequencing (WES)
Starting at $600.00 per sample

We used the Agilent SureSelect WES V6+UTR capture kit. Typically we target >50-100x coverage per sample with pair end sequencing (PER125). This if the cost for library preparation only, sequencing is not included.

Deliverables: Raw and quality filtered data, alignment files, SNP and InDel calls using SAM tools.

We used the Agilent SureSelect WES V6+UTR capture kit. Typically we target >50-100x coverage per sample with pair end sequencing (PER125). This if the cost for library preparation only, sequencing is not included.

Deliverables: Raw and quality filtered data, alignment files, SNP and InDel calls using SAM tools.

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QuantStudio 12K Flex
Agilent SureSelect
Illumina Sequencing
Starting at $1,070.00 per lane

Single End Read (SER) [Illumina HiSeq2500v4], per lane price
Sequencing 1x50: $1,070.00
Sequencing 1x100: $1,392.00

Pair End Read (PER) [Illumina HiSeq2500v4], per lane price
Sequencing 2x50: $2,005.00
Sequencing 2x125: $2,651.00
Sequencing 2x150: $3,181.00
Sequencing 2x250: $3,903.00

Sequencing costs include basic... Show more »

Single End Read (SER) [Illumina HiSeq2500v4], per lane price
Sequencing 1x50: $1,070.00
Sequencing 1x100: $1,392.00

Pair End Read (PER) [Illumina HiSeq2500v4], per lane price
Sequencing 2x50: $2,005.00
Sequencing 2x125: $2,651.00
Sequencing 2x150: $3,181.00
Sequencing 2x250: $3,903.00

Sequencing costs include basic data analysis:
* Demultiplexing
* Read processing (filtering based on complexity and end trimming based on quality scores)
* Mapping to reference genome
* Differential expression analysis

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QuantStudio 12K Flex
Nextera Library Preparation
Starting at $90.00 per sample

Instrumentation: Illumina HiSeq2500 or MiSeq

Sample requirements:
If providing tissue, blood or cells, we require enough material to obtain at least 2ug of total gDNA. For purified gDNA, we recommed submiting at least 2ug of purified total gDNA in ultra pure water. Sample quantity and quality will be verified with... Show more »

Instrumentation: Illumina HiSeq2500 or MiSeq

Sample requirements:
If providing tissue, blood or cells, we require enough material to obtain at least 2ug of total gDNA. For purified gDNA, we recommed submiting at least 2ug of purified total gDNA in ultra pure water. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and gel electropheresis. We recommend DNA purity with an OD260/280=1.8-2.0 without degradation or RNA contamination.

« Show less
QuantStudio 12K Flex
ChIP-Seq Library Preparation
Starting at $280.00 per sample

ChIP-seq Library Preparation:

We use the Illumina HiSeq2500 for the majority of our ChIP-seq projects.

Sample requirements:
Please submit at least 20-50ng of ChIP or capture kit enriched DNA in ultra pure water. We strongly recommend verification of the ChIP samples with qPCR prior to submission for ChIP-seq library... Show more »

ChIP-seq Library Preparation:

We use the Illumina HiSeq2500 for the majority of our ChIP-seq projects.

Sample requirements:
Please submit at least 20-50ng of ChIP or capture kit enriched DNA in ultra pure water. We strongly recommend verification of the ChIP samples with qPCR prior to submission for ChIP-seq library contruction. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and the Agilent Bioanalyzer 2100 profile. We recommend DNA purity with an OD260/280=1.8-2.0 without RNA contamination and a size profile of 200-500bp.

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QuantStudio 12K Flex
Illumina HiSeq 2500
NGS Data Analysis
Next generation sequencing data analysis
Starting at $125.00 per hour

Raw data processing to remove low quality reads, alignment to reference genome using SHRIMP2 or BWA, and differential expression analysis using CuffDiff2 or EdgeR. We also can provide de novo assembly construction.

Raw data processing to remove low quality reads, alignment to reference genome using SHRIMP2 or BWA, and differential expression analysis using CuffDiff2 or EdgeR. We also can provide de novo assembly construction.

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QuantStudio 12K Flex
Truseq DNA Library Preparation
Starting at $284.00 per sample

TruSeq DNA-seq (Nano kit): $284.00
TruSeq PCR-free DNA: $294.00

Sample requirements: 250ng DNA for Nano or 2ug DNA for PCR-Free library.

Sample requirements:
If providing tissue, blood or cells, we require enough material to obtain at least 0.250 - 2ug of total gDNA. For purified gDNA, we recommed submiting at least... Show more »

TruSeq DNA-seq (Nano kit): $284.00
TruSeq PCR-free DNA: $294.00

Sample requirements: 250ng DNA for Nano or 2ug DNA for PCR-Free library.

Sample requirements:
If providing tissue, blood or cells, we require enough material to obtain at least 0.250 - 2ug of total gDNA. For purified gDNA, we recommed submiting at least 0.250 - 2ug of purified total gDNA in ultra pure water. Sample quantity and quality will be verified with spectrophotometry (NanoDrop 1000), fluorometry (Qubit), and gel electropheresis. We recommend DNA purity with an OD260/280=1.8-2.0 without degradation or RNA contamination.

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QuantStudio 12K Flex
RNA Extraction and Purification
Starting at $32.00 per sample

Trizol: $40.00 per sample
Qiagen: $32.00 per sample

Trizol: $40.00 per sample
Qiagen: $32.00 per sample

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QuantStudio 12K Flex
RNA Quality Control
Starting at $18.00 per sample

Includes Nanodrop or Qubit, and Agilent Bioanalyzer 2100 analysis

Includes Nanodrop or Qubit, and Agilent Bioanalyzer 2100 analysis

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Agilent Bioanalyzer
Qubit 2.0 fluorometer
NanoDrop 2000
QuantStudio 12K Flex
16S rRNA Sequencing
Starting at $60.00 per sample

The listed price is includes library construction, pooling, MiSeq 2x300 run, and data analysis through OTU table generation. MiSeq runs only with or without analysis is an option.

Instrumentation: Illumina MiSeq

We can multiplex up to 200 samples per run and we use v3 2x300 Illumina MiSeq reagents.

Turnaround... Show more »

The listed price is includes library construction, pooling, MiSeq 2x300 run, and data analysis through OTU table generation. MiSeq runs only with or without analysis is an option.

Instrumentation: Illumina MiSeq

We can multiplex up to 200 samples per run and we use v3 2x300 Illumina MiSeq reagents.

Turnaround time: ~4-6 weeks including 16s library construction (DNA is provided) or 3-4 weeks for just the MiSeq run. Other cycle options are available depending on need.

Deliverables:

  • Raw data through OTU table data.
  • Secondary analysis can be performed using our NGS Data analysis service.

We use the protocol described here for 16s Metagenomic Analysis:

Fadrosh et al.
Microbiome. 2014 Feb 24;2(1):6. doi: 10.1186/2049-2618-2-6.

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QuantStudio 12K Flex
Digital PCR
Price on request
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QuantStudio 12K Flex
Plasmid Sequencing
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Genotyping Services
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Sequencing of PCR Amplicons
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DNA Sequencing
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DNA Fragmentation Assays
Price on request
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Deep Sequencing
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Amplicon Sequencing
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Biology
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Cell-Based Assays
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Cell Death Assays
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Biochemistry & Molecular Biology
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Biomolecular Interaction Analysis
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Protein-DNA Interaction Analysis
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Nucleic Acid Services
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Nucleic Acid Analysis
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Nucleic Acid Data Analysis
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Sequencing Data Analysis
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DNA Services
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Next Generation Sequencing (NGS)
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DNA Library Construction Services
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Targeted Gene Sequencing
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Exome Sequencing Services
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Epigenetic Studies
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PCR
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RNA Services
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RNA Sequencing
Price on request
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2018-07-03 09:12:05 -0700

Net Promoter Score of 8 received for Single Cell RNA-Seq.

Additional Ratings: satisfaction with deliverable: 9, satisfaction with timeliness: 8.
March 10, 2017

Positive review received for Low Input/Single Cell RNA Sequencing:

"Great service! I had an opportunity to discuss over the phone the details of my project which was important to me. Results are of very high quality. Thanks! Vasily."

October 21, 2016

Positive review received for Low Input/Single Cell RNA Sequencing:

"Quick service, through study and reasonable price. I think this is great!"

2016-08-04 13:16:30 -0700

Net Promoter Score of 10 received for Low Input/Single Cell RNA Sequencing.

Additional Ratings: satisfaction with deliverable: 10, satisfaction with timeliness: 10.
April 15, 2015

Positive review received for RNA Sequencing:

"John is a great guy and everything else is good."

October 13, 2014

Positive review received for RNA Sequencing:

"I highly recommend John and his group. The quote was very reasonable in terms of its cost, and the quality of analysis was superb. The analysis was done very professionally and much faster than we expected. Thank you! I would definitely use this service again."

May 27, 2014

Positive review received for RNA Sequencing:

"Yes I would"

February 12, 2014

Positive review received for RNA Sequencing:

"John was great."

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