Instrumentation & Services

Core Provide training for all shared instruments, and they are operated under Self Service. Please use this link https://ppms.us/salk/listsys/?pf=9 to book those instruments on PPMS

Agilent TapeStation 4150

Agilent TapeStation 4150 for measuring DNA

Nucleic Acid	Tape Station Assay	Description	Concentration Range (ng/μl)	Size Range (bp)
RNA	RNA Tape	RNA Screen Tape	5-500	50-600
RNA	HS RNA Tape	High Sensitivity RNA Screen Tape	0.1-10	50-600
DNA	DNA Tape	D1000/D5000 Screen Tape	0.1-50	35-1000
	HS DNA Tape	High Sensitivity D1000/D5000 Screen Tape	0.01-1	35-1000
	Genomic Tape	Genomic DNA Screen Tape	10-100	200-15000

Qubit 3.0 Fluorometer

Qubit 3.0 Fluorometer for measure DNA or RNA concentration with all the reagents provided. Remember to sign out the reagents usages when finished.

Nucleic Acid	Qubit Assay	Description	Concentration Range (ng/μl)	Sample Types
RNA	BR RNA	Qubit Broad Range RNA	5-1000	RNA
RNA	HS RNA	Qubit High Sensitivity RNA	0.25-100	RNA from limited samples
DNA	BR DNA	Qubit Broad Range DNA	0.1-1000	Genomic, dsDNA
DNA	HS DNA	Qubit High Sensitivity DNA	0.1-100	dsDNA, ChIP

QuantStudio 3 and 5 Real-Time PCR Systems

QuantStudio 3 and 5 Real-Time PCR Systems can detect differences in target quantity as low as 1.5-fold, support 96-well (0.2ml or 0.1ml) or 384-well (QS5 only) consumables. The recharge is linked to the time it was booked.

Tecan Infinite® 200 Plate reader

Tecan Infinite® 200 Plate reader for measuring fluorescence, luminescence or absorbance detection with an advanced quad-4 monochromators™ system (M200). It has the i-control™ software for easy set up protocols, and optional Magellan™ software packages provide full data reduction capability. It is no charge for using it if you set it up with your own consumables.

Full Service_Short read Illumina Platform Library Preparation and Sequencing

Library Construction: Core offers the following library construction as standard services

TruSeq Stranded mRNA (PolyA+)

Submission Instruction: Please provide >1 µg of total RNA with concentration between 50–200 ng/µl, RIN > 8

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop concentration and submit 5 µl of samples in 8-well PCR strip tubes for QC
Please submit stock samples in 8-well PCR strip tubes with individually attached caps. (USA Scientific. #1402-4700).
6. Please save your completed form in the format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project.
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

TruSeq Stranded Total RNA Gold

Submission Instruction: Please provide >1ug of total RNA with concentration between 50-200ng/ul, RIN>8.

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop

(Don’t cut 8-strips and do not skip any well)

Please submit stock samples in 8-well PCR strip tubes with individually attached caps. (USA Scientific. #1402-4700).
Please save your completed form in the format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

Ultra Low mRNA (SMART-Seq mRNA HT LP)

Submission Instruction: Please provide 10pg-1ng of total RNA with concentration < 1ng/uL, RIN>8.

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop concentration and submit 5 µl of samples in 8-well PCR strip tubes for QC (Don’t cut 8-strips and do not skip any well)
Please submit stock samples in 8-well PCR strip tubes with individually attached caps. (USA Scientific. #1402-4700).
Please save your completed form in the format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

Illumina DNA Prep

Submission Instruction: Please provide >100ng of DNA with concentration 5-50 ng/ul with A260/280=1.8-2.0, A260/230=2.0-2.2

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop concentration and submit 5 µl of samples in 8-well PCR strip tubes for QC (Don’t cut 8-strips and do not skip any well)
Please submit stock samples in 8-well PCR strip tubes with individually attached caps. (USA Scientific. #1402-4700).
Please save your completed form in the format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

NEBNext Ultra II DNA (ChIP, Amplicon, <400bp) Prep (no fragmentation)

Submission Instruction: Please provide > 5 ng of DNA with concentration > 0.2 ng/uL with A260/280=1.8-2.0, A260/230=2.0-2.2

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop concentration and submit 5 µl of samples in 8-well PCR strip tubes for QC (Don’t cut 8-strips and do not skip any well)
Please submit stock samples in 8-well PCR strip tubes with individually attached caps. (USA Scientific. #1402-4700).
Please save your completed form in the format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

Sequencing: Core uses the following sequencers to address different coverages with different costs and turnaround time.

Novaseq X plus

Flow Cell Types
Flow Cell Type	Total Lanes (per flow cell)	Output (whole flowcell)	Kits options (per flow cell)
1.5B	2	1.5B	100 cycles (max. 138 cycles) 200 cycles (max. 238 cycles) 300 cycles (max. 238 cycles)
10B	8	10B	100 cycles (max. 138 cycles) 200 cycles (max. 238 cycles) 300 cycles (max. 238 cycles)
25B	8	25B	300 cycles (max. 338 cycles)

Nextseq 2000

Nextseq 2000
Flow Cell Type	Total Lanes (per flow cell)	Output (whole flowcell)	Kits options (per flow cell)
P1	1	100M	100 cycles kit (max. 138 cycles) 300 cycles kit (max. 338 cycles) 600 cycles kit (max. 638 cycles)
P2	1	400M	100 cycles kit (max.138 cycles) 200 cycles kit (max.238 cycles) 300 cycles kit (max. 338 cycles)
P3	1	1.1B	50 cycles kit (max. 88 cycles) 100 cycles kit (max.138 cycles) 200 cycles kit (max.238 cycles) 300 cycles kit (max. 327 cycles)

Miniseq

Miniseq
Flow Cell Type	Total Lanes (per flow cell)	Output (whole flowcell)	Kits options (per flow cell)
HighOutput	1	22–25 M	75 cycles kit (max. 92 cycles) 150 cycles kit (max.168 cycles) 300 cycles kit (max.318 cycles)
MidOutput	1	7–8 M	300 cycles kit (max.318 cycles)

Full Service_Long Read PacBio Platform Library Preparation and Sequencing

Library Construction: Core offers the following library construction as standard services:

Iso-Seq (full length transcript RNA-Seq)

Submission Instruction:

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop concentration and submit 5 µl of samples in 8-well PCR strip tubes for QC (Don’t cut 8-strips and do not skip any well)
Please submit stock samples in 1.5 mL Eppendorf tubes (low binding preferred) with sample code written on top of tube.
Please follow this table to prepare your samples

Please refer to this table to prepare your samples
Input	Total Input	Concentration	QC	Comments
Total RNA	> 300ng	50-200 ng/µl	A260/280=1.8-2.0 A260/230=2.0-2.2 RIN > 7	Resuspend in RNase-free water
cDNA	> 1 µg		cDNA Profile (Tapestation or Bioanalyzer)	Resuspend in EB or low EDTA TE

Please save the form in format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

Whole Genome Sequencing 15Kb HiFi

Submission Instruction:

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop concentration and submit 5 µl of samples in 8-well PCR strip tubes for QC (Don’t cut 8-strips and do not skip any well)
Please submit stock samples in 1.5 mL Eppendorf tubes (low binding preferred) with sample code written on top of tube.
Please follow this table to prepare your samples

Please refer to this table to prepare your samples
Input	Total Input	Concentration	QC	Comments
HMW gDNA	> 2µg	50-100 ng/µl	A260/280=1.8-2.0 A260/230=2.0-2.2	Resuspend in EB or low EDTA TE. **DNA should be at high quality and sufficient quantity since there is no amplification step.

Please save your completed form in format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

PureTarget repeat expansion panel

Submission Instruction:

Download the form and follows the instructions to fill the form.
Sample codes should be identical as the labels on the tube with your initials and sequential numbers. (Always start with 1 and do not skip number. i.e., NGS1, NGS2, NGS3, etc.)
Sample Name can ONLY be named with alphabets, numbers, underscores, and not more than 20 characters respectively. (No space, +.,!@#$%^& etc.)
Please fill in Qubit and Tape station results on the form if available. Otherwise, please provide nanodrop concentration and submit 5 µl of samples in 8-well PCR strip tubes for QC (Don’t cut 8-strips and do not skip any well)
Please submit stock samples in 1.5 mL Eppendorf tubes (low binding preferred) with sample code written on top of tube.
Please follow this table to prepare your samples

Please refer to this table to prepare your samples
Input	Total Input	Concentration	QC	Comments
HMW gDNA	> 2µg	50-100 ng/µl	A260/280=1.8-2.0 A260/230=2.0-2.2	EB, low EDTA TE (pH8)

Please save your completed form in format of YYMMDD_PI_YourFirstName_LibrarySEQ_Form and upload it to https://ppms.us/salk/?IGC under request/start a new project
Drop off samples Tuesday/Thursday between 10am-12pm with dry ice and sign the drop off sheet on the drop off bench.

Sequencing: We use the lasted technology Revio for fast turnaround time and getting the reliable data.

HiFi Sequencing Performance
Library	Run time*	Q30+ bases	HiFi yield per SMRT Cell	Methylation
1–5 kb	12 hours	95%	6–8 million reads
5–10 kb			35–70 Gb
10–15 kb	24 hours	90%	70–100 Gb
15–20 kb			100–120 Gb
20–25 kb	30 hours	85%	100–120 Gb	5mC at CpG sites and 6mA^† for native DNA

Key Applications and Sample Throughput with SPRQ Chemistry
Library	Application	Per Revio SMRT Cell	Expected coverage
1–5 kb	Amplicon sequencing	>1,000	50×
5–10 kb	Microbial genome	384	30×
5–10 kb	PureTarget repeat expansion panel	48	200×
15–20 kb	Human genome	2	20×
15–20 kb	Human methylation profiling	8	5×
15–20 kb	Transcriptome with Kinnex™ full-length RNA kit	6	10 million reads

Full Service_Long Read NanoPore Platform Library Preparation and Sequencing

More information coming soon.

The Razavi Newman
Integrative Genomics and Bioinformatics Core

Salk Institute for Biological Studies - The Razavi Newman
Integrative Genomics and Bioinformatics Core - Instrumentation and Services

Instrumentation & Services

The Razavi NewmanIntegrative Genomics and Bioinformatics Core

Salk Institute for Biological Studies - The Razavi NewmanIntegrative Genomics and Bioinformatics Core - Instrumentation and Services

Instrumentation & Services

The Razavi Newman
Integrative Genomics and Bioinformatics Core

Salk Institute for Biological Studies - The Razavi Newman
Integrative Genomics and Bioinformatics Core - Instrumentation and Services