Pacific Biosciences Accuracy Notes

DateOverallInsertionsDeletionsSubstitutionsRead LengthRef
PacBio RS II~2013~11%“predominantly indel”“predominantly indel”“predominantly indel”Vendor
PacBio RS II2020~13%8%3%1.68%Academic Benchmark
PacBio RS II CLR202012.88%8.04%3.16%1.68%8899Academic Benchmark
PacBio RS II Subread201714.2%5.92%3.01%5.27%Academic Benchmark
PacBio Sequel I CLR201912%Inferred from Vendor Claim
PacBio Sequel II CLR201910%~50KbInferred from Vendor Claim
Revio (Subread)202310%All: 100Kb+?Inferred from Vendor Claim
PacBio RS II CCS20171.720.087%0.34%1.3%1772Academic Benchmark
PacBio Sequel HiFi20220.25%0.1%0.13%0.02%Academic Note
PacBio Sequel II CCS20190.14%Academic Benchmark
PacBio Sequel  II HiFi2019<0.1%20KbVendor Claim
Revio (All HiFi)2023<0.1%16.5KbVendor Claim

Random Notes 5

Xaar 128

chinese inkjet info:

RNA Bioanalyzer

PaperQuantification pg/ul RNARunPlots
Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols397.5 ng/60 mL (Qubit RNA HS)Agilent 4200 TapeStationRIN: 5.9An external file that holds a picture, illustration, etc. Object name is nihms918280f3b.jpg
Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols397.5 ng/60 mL(Qubit RNA HS)Agilent 4200 TapeStationRIN: 3.3An external file that holds a picture, illustration, etc. Object name is nihms918280f3a.jpg
Deep Sequencing of Urinary RNAs for Bladder Cancer Molecular Diagnostics0.98 ng/mL0.08 ng/mLProcessed within two hours of collectionAgilent 2100 Bioanalyzer, RNA Pico chipsRIN ranged from 2.5 to 9.5Mean: 6.03No plots
Identification of microRNAs in blood and urine as tumour markers for the detection of urinary bladder cancer~2 ng/uL (fig. 1)Several urine RNA isolates showed low RIN values <3No plots
Urinary MicroRNA-Based Diagnostic Model for Central Nervous System Tumors Using Nanowire ScaffoldsQubit microRNA AssayAgilent 2100 BioanalyzerRIN: 81638356162683-129.png

RNA Papers

SingleMol Imaging

Solid state Nanopore

Hitachi, making pores with dialectric breakdown, slowing, notes on viscosity to slow etc:

Keio University group, optical observation of translocation:


ASIC Design, to go to 1MHz:

Noise measurements from above:

Instrumentation for Low-Noise High-Bandwidth Nanopore Recording. Engineered Nanopores for Bioanalytical Applications:

Above has lots of nice protocol information.

Ionic Speed/Current

“If we recall that an Ampere corresponds to a charge flow of 1 Coulomb each second and further, use the fact that the charge on a monovalent ion is approximately 1.6 x 10-19 Coulombs (that is 1 electron or 1 proton charge), then we see that a current of about one pA corresponds to roughly 107 ions passing through the channel each second. This value is in agreement with measurements”

Molecular Dynamics of Ionic Current:

DNA Speed:
From, measures time to translocate two adjacent pores. distance is ~1.5um:

Folded/Knotted DNA:

Detection of knotted DNA


Double stranded Lambda DNA (16um long, 48kb). Translocates in 3 different confirmations. Grabbed at the end. Grabbed in the middle (completely folded), Grabbed near an edge (partly folded). Difference in current levels is ~1nS between each confirmation (200pA). 22nm pore is used. Translocation time ~3ms.

Hairpins, P2000 pulled quartz nano-pipette. Using hairpins to encode DNA 8bp and 16bp hairpins.

DNA Folds for data storage by Ulrich:

Unknown rotary valve (from Affy fluidics)

BW Spectrometer Notes

  • Meanwell PS45-5 40Watt 5V 8Amp open frame power supply
  • Astrodyne OFM-0201 5V 4.4 Amp power supply
  • Spectrometer control board
  • B&W Tech fiber optic input spectrometer without TE cooling. Internal baffles will have to be removed to get the full spectrometer range, serial port output.
  • OD6025-05HB 5V ball bearing fan.
  • Keyswitch (key not included)
  • Optical beamsplitter with assembly with lenses, beam splitter, fiber couplings

useful spectra:
Peak numberWavelength of peak (nm)Species producing peakActual line location (nm)
3487.7terbium from Tb3+~485 to 490
4542.4terbium from Tb3+~543 to 544
6577.7likely terbium from Tb3+ or mercury576.960 for Hg or ~578 for Tb
7580.2mercury or terbium from Tb3+579.066 for Hg or ~580 for Tb
8584.0possibly terbium from Tb3+ or europium in Eu+3:Y2O3~580
9587.6likely europium in Eu+3:Y2O3~587
10593.4likely europium in Eu+3:Y2O3~593
11599.7likely europium in Eu+3:Y2O3~598
12611.6europium in Eu+3:Y2O3~611
13625.7likely terbium from Tb3+~625
14631.1likely europium in Eu+3:Y2O3~630
15650.8likely europium in Eu+3:Y2O3~650
16662.6likely europium in Eu+3:Y2O3~661
17687.7likely europium in Eu+3:Y2O3~687-688
18693.7likely europium in Eu+3:Y2O3~693
19707 and 709likely europium in Eu+3:Y2O3~707 and ~709
20712.3likely europium in Eu+3:Y2O3~712
21760.0likely argon758.9315 or 763.5106 (??)
22811.0likely argon811.531

General spectrometer info


Hg Lines:

Hg Lines:

Wavelength (nm)Name (see photoresist)Color
184.45 ultraviolet (UVC)
253.7 ultraviolet (UVC)
365.4I-lineultraviolet (UVA)
546.1 green
578.2 yellow-orange

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