DNA/RNA QC Samples per Chip=12 RNA Nano chip: Qualitative Range=5-500 ng/µL, Quantitative range: 25-500ng/µL (Total RNA Assay), 25-250ng/µL (mRNA Assay) DNA 1000 chip: Quantitative Range=0.5-50 ng/µL, DNA Sizing Range=25-1000 bp DNA 7500 chip: Quantitative Range=0.5-50 ng/µL, DNA Sizing Range=100-7500 bp DNA 12000 chip: Quantitative Range=0.5-50 ng/µL, DNA Sizing Range=100-12000 bp

DNA/RNA QC – High Sensitivity Samples per Chip=11 RNA Pico chip: Qualitative Range=50-5000 pg/µL, Quantitative range=50-5000pg/µL (Total RNA Assay), 250-5000pg/µL (mRNA Assay) DNA High Sensitivity chip: Quantitative Range=5-500 pg/µL, DNA Sizing Range=50-7000 bp

Windows users:

\\smb.files.pennstatehealth.net\cores\ResultsDropoffPickup\GenomeSciences\Results

 

If you are accessing from Mac, there are 3 different possible ways to access your Core folder from your MacBook determined by HOW you login to your Macbook.

1.     You login with a local computer account NOT associated with your epass id.

2.     You login with an epass account and your Macbook is part of the PennStateHealth domain.*

3.     You login with an epass account and your Macbook is part of the Hersheymed domain.*

Please proceed to the appropriate section for your situation:

—————————————-Scenario 1—————————————-

In Finder, select Go…Connect to Server.

Enter:

smb://smb.files.pennstatehealth.net/cores

When prompted, enter your epass id and password.

 

 

—————————————-Scenario 2—————————————-

In Finder, select Go…Connect to Server.

Enter:

smb://smb.files.pennstatehealth.net/cores

You should not be prompted, and your lab folder should connect automatically.

 

 

—————————————-Scenario 3—————————————-

In Finder, select Go…Connect to Server.

Enter:

smb://*:*@smb.files.pennstatehealth.net/cores

When prompted, enter your epass in this format: (reference screenshot on next page)

<epass>@adds.pennstatehealth.net and then your current epass password.

Since we often get asked, here is a quick reference for MiSeq (we have two), NextSeq (UP Core has one), and NovaSeq (we have one).

flow cell type	read#	read length
MiSeq Reagent Kit v2	12-15 million	1 × 36 bp	2 × 25 bp	2 × 150 bp	2 × 250 bp
MiSeq Reagent Kit v3	22–25 million	2 × 75 bp	2 × 300 bp
MiSeq Reagent Kit v2 Micro	4 million	2 × 150 bp
MiSeq Reagent Kit v2 Nano	1 million	2 × 150 bp	2 × 250 bp
NextSeq 550 System Mid-Output Kit*	130 Million	2 × 75 bp	2 × 150 bp
NextSeq 550 System High-Output Kit*	400 Million	1 × 75 bp	2 × 75 bp	2 × 150 bp
NovaSeq SP	650–800 Million	2 × 50 bp	2 × 100 bp	2 × 150 bp	2 x 250 bp
NovaSeq S1	1.3–1.6 Billion	2 × 50 bp	2 × 100 bp	2 × 150 bp
NovaSeq S2	3.3 B–4.1 Billion	2 × 50 bp	2 × 100 bp	2 × 150 bp
NovaSeq S4	8-10 Billion	1 × 35 bp	2 × 100 bp	2 × 150 bp
*: available at UP Genomics Core

Since I get asked often but the official workflow is not made available in our iLab portal yet, please find below description handy to plan your 10X Genomics’s single-cell RNA-seq projects!

 

The library prep cost can be found in the iLab:

10x Genomics Library Prep Single Cell RNA-Seq 3P Library Prep (V3, per sample, sequencing not included)

initiate request $1,713.00 (Internal)

For RNA-seq we sequence 20K reads per sample for up to 10K cells per the prep, so ~200M reads by NovaSeq 100 cycles will also need to be requested.

NovaSeq_SP ( 100 cycles – SR100, PE 2×50 ) (per flow cell) Per flow cell

initiate request $2,751.38 (Internal)

is the smallest flowcell you will likely be using and it can hold ~750M reads. Even you occupy 400M reads, we will have to find someone else to fill up the rest of 350M. Depending on how soon you would like the sequence goes, you may have to pay more $ to fill up the flow cell.