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Extractions (DNA or RNA)

Sample Type	Input Requirements*	Price
Cells	0.5-10 million cells	$32.00
Tissue	5-30mg tissue	$32.00
Paraffin-embedded (FFPE) Tissue	Please provide three 5mm sections	$47.00
Saliva	Sample provided in a DNAGENOTEK Saliva-based collection tube	$47.00
Blood/Serum/Plasma/Buffy Coat	Sample provided in BD Vacutainer Blood Collection tube(www.bd.com), Paxgene tube, or Tempus tube Note: please follow manufacturer protocol/recommendations for each tube type	$47.00

*Input requirements are recommended. If your sample amount is limited, contact us to discuss options.

Library Preparation - Input Requirements

RNA Library Preparation	Input Quantity Range	RNA Integrity (RIN) Score	Min Concentration
Illumina Stranded Total Ligation (Ribo-Zero Plus)	10-1000 ng	RIN > 2	1 ng/µl
Illumina Stranded mRNA (PolyA+)	25-1000 ng	RIN ≥ 8	1 ng/µl
SMARTer TCR Profiling (Human/mouse)	10-250 ng	RIN > 7	1 ng/µl
SMART-Seq Stranded Total RNA (Ultra Low Input)	1-10 ng	RIN > 2	0.13 ng/µl
SMART-Seq HT Ultra Low Input	1-10 ng	RIN ≥ 8	0.2 ng/µl
QIAseq small RNA	1-500 ng	RIN ≥ 8	0.2 ng/µl
DNA Library Preparation
Nextera DNA XT (low input)	1 ng cDNA		0.2 ng/µl
Illumina DNA Prep (Nextera FLEX)	1-500 ng cDNA		0.2 ng/µl
Illumina DNA PCR-Free Prep (WGS)	25-300 ng DNA		1 ng/µl
ChIP-seq (Library prep only)	5-10 ng CHIP DNA		0.1 ng/µl
ATAC-Seq	10k-50k cells

Library Generation

Illumina Stranded Total Ligation (Ribo-Zero Plus)
Total RNA input is depleted using enzymatic depletion method that removes abundant transcripts from total RNA. Random primers initiate first and second strand cDNA synthesis. Adenylation of 3' ends are followed by adapter ligation and library amplification with indexing. 

This method is used when you want to characterize long non-coding RNA (lncRNA) as well as mRNA. It is compatible with degraded RNA as there is no poly-A enrichment.

Illumina Stranded mRNA (PolyA+)
Total RNA input is enriched for mRNA molecules containing polyA tails using Oligo(dT) magnetic beads. The purified mRNA is fragmented, and random primers initiate first strand and second strand cDNA synthesis. Adenylation of 3' ends are followed by adapter ligation and library amplification with indexing. 

This method is used in transcriptome or gene expression studies.

SMARTer TCR Profiling (Human/mouse)
Used to analyze T-cell receptor (TCR) diversity from total (bulk) RNA samples and whole cells. cDNA is synthesized using TCR dT primers. Two rounds of PCR are performed to amplify cDNA sequences. In the second PCR, forward and reverse primers are added including adapter and index sequences.

SMART-Seq Stranded for Total RNAseq (Ultra Low Input)
Reverse transcription with random primers and template switching generates first strand cDNA. cDNA is amplified using the template switching adapter and a sequence added to the random primers. Ribosomal cDNA is cleaved and the uncleaved fragments are amplified with indexed primers. This method is used with low quality and quantity RNA samples.

SMART-Seq mRNA HT (Ultra Low Input) – for flow sorted cells
SMART-Seq HT ultra-Low input RNA Kit – prepare ds-cDNA  

Reverse transcription with oligo(dT) primers and template switching oligo generates first strand cDNA. cDNA is amplified using the template switching adapter and a sequence added to the polyT primer. 

This kit is used for very low input RNA and/or direct flow sorted samples.

Illumina Nextera XT
Tagmentation with transposase fragments DNA and incorporates shortened Illumina adapters. Indexes are added via index PCR.

Illumina DNA Prep (previously named: Nextera FLEX)
Tagmentation using enzymatic reaction to fragment DNA and add adapter sequences. Indexes are added via index PCR.

Illumina DNA PCR-free
Tagmentation using enzymatic reaction to fragment DNA and add adapter sequences. Indexes are added via direct ligation. Used for whole genome sequencing (WGS).

Lexogen 3'-Quantseq
QuantSeq kits enable cost-efficient sequencing by counting (differential gene expression only). These kits are an alternative to standard Total RNA-Seq from highly degraded low-input samples. Library is generated from 3'-ends only. Not recommended for lncRNA and isotype variants.

QIAseq small RNA
Pre-adenylated adapter is ligated to the 3' end of small RNAs followed by 5' ligation of an RNA adapter. cDNA synthesis is completed using a reverse transcription (RT) primer targeted to the 3' pre-adenylated adapter. Unique molecular indices (UMIs) are integrated into the RT primer to assign a unique identifier to each miRNA molecule. Indexes are added via index PCR.

ChIP-seq (Library prep only)
The goal of this protocol is to add adapter sequences onto the ends of ChIP DNA to generate indexed libraries.

ATAC-Seq/Omni-ATAC-seq
Assay for transposase-accessible chromatin sequencing to identify regions of open chromatin. In the tagmentation process, Tn5 transposase fragments open genomic DNA and inserts sequencing primers into chromatin open regions. Data analysis from sequencing provides understanding of gene regulation.

Illumina Sequencing

MiSeq Flow Cells	Number of Reads	Cycles	Typical Run Type	Price
Micro	4 million	300	2x150bp	$620
V2	13 million	50	1x50bp	$1,180
		300	2x150bp	$1,460
V3	25 million	150	2x75bp	$1,280
		600	2x300bp	$2,050
NextSeq 2000 Flow Cells	Number of Reads	Cycles	Typical Run Type	Price
P1	100 million	100	2x58bp	$1,300
		600	2x300bp
P2	400 million	100	2x58bp	$1,900
		200	2x100bp	$3,450
		300	2x150bp	$4,480
P3	1.2 billion	50	1x50bp, 2x35bp	$3,100
		100	2x58bp	$4,000
		200	2x100bp	$5,600
		300	2x150bp	$7,350

Single Cell Technologies

3' Gene Expression
Gene expression of up to 10,000 cells per sample. Multiplexing options include cell hashing with antibody labelling or CellPlex lipid tags.

5' Gene Expression and Immune Profiling
Gene expression, TCR and BCR profiling of up to 10,000 cells per sample. Multiplexing available with antibody-based cell hashing.

Gene Expression Flex
A probe-based assay that can be used to profile fixed tissues and cells (including cells isolated from FFPE). Tissues and cells can be stored up to 6 months at -80C. Multiplexing available for up to 16 samples. Compatible with human and mouse.

CITE-Seq
Barcoded antibodies bind to surface markers on individual cells. The barcode marker sequence carries over through the library preparation, permitting quantitative assessment of surface antibody binding to cells along with their transcriptome information. Hundreds of surface antigens can be assayed simultaneously.

Multiome ATAC and Gene Expression
Provides simultaneous detection of mRNA and chromatin accessibility from the same cell.

For more information, please visit https://singlecell.pitt.edu/

Spatial Transcriptomics

10X Visium Spatial Gene Expression

For additional information: https://www.10xgenomics.com/products/spatial-gene-expression 

Sample Type	Tissue Size	Samples per Slide	Staining Options	Cost (Sequencing not included)
Fresh Frozen	6.5mm x 6.5mm	4	H&E, Immunofluorescence (4 colors max)	$6,200 + $1,200 for tissue permeabilization (required)
CytAssist Fresh Frozen	6.5mm x 6.5mm	4	H&E only	$8,400
CytAssist Fresh Frozen	11mm x 11mm	2	H&E only	$8,600
CytAssist FFPE	6.5mm x 6.5mm	4	H&E, Immunofluorescence (4 colors max)	$8,400
CytAssist FFPE	11mm x 11mm	2	H&E, Immunofluorescence (4 colors max)	$8,600

Curio Biosciences Slide Seeker

For additional information: https://curiobioscience.com/ 

Sample Type	Tissue Size	Samples per Slide	Staining Options	Cost
Fresh Frozen	3mm x 3mm	1	None for transcriptome section – serial sections for staining recommended	Please contact
Fresh Frozen	10mm x 10mm	1	None for transcriptome section – serial sections for staining recommended	Please contact