Archive for the ‘Uncategorized’ Category.

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

https://github.com/MatthiasWM/Xaar128

https://github.com/gkyle/xaar128

https://www.xaar.com/en/products/xaar-printheads/xaar-128/

http://ytec3d.com/forum/viewtopic.php?t=47

chinese inkjet info: http://m.6lon.com/sdm/132165/2/cp-1003311/0.html

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: https://www.nature.com/articles/srep31324.pdf

Keio University group, optical observation of translocation: https://iopscience.iop.org/article/10.7567/APEX.9.017001/pdf


Amplification/Electronics

ASIC Design, to go to 1MHz: https://www.nature.com/articles/nmeth.1932

Noise measurements from above:

Instrumentation for Low-Noise High-Bandwidth Nanopore Recording. Engineered Nanopores for Bioanalytical Applications: https://www.sciencedirect.com/science/article/pii/B9781437734737000030

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” http://book.bionumbers.org/how-many-ions-pass-through-an-ion-channel-per-second/

Molecular Dynamics of Ionic Current: https://www.ks.uiuc.edu/Research/silica/IonRect.html

DNA Speed:
From, measures time to translocate two adjacent pores. distance is ~1.5um: https://pubs.acs.org/doi/full/10.1021/nl2030079

Folded/Knotted DNA:

Detection of knotted DNA

https://www.nature.com/articles/nnano.2016.153

https://www.nature.com/articles/s41467-019-12358-4

Folding

https://www.ncbi.nlm.nih.gov/pubmed/20608744

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.

https://pubs.acs.org/doi/pdf/10.1021/acs.nanolett.8b04715

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

DNA Folds for data storage by Ulrich: https://www.ncbi.nlm.nih.gov/pubmed/30585490


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

http://www.excaliburmineral.com/Aramis2/473nm/spectro/index.htm

http://www.excaliburmineral.com/Aramis2/473nm/index.htm

https://www.ebay.com/itm/162959836456?ViewItem=&item=162959836456

https://laserpointerforums.com/f42/b-wtech-473nm-unit-spectrometer-mods-info-101467.html

https://alexanderimpertro.wordpress.com/2015/10/27/bw-tek-bwb-10-oem-473nm-blue-lab-style-dpss-laser/

useful spectra: https://en.wikipedia.org/wiki/User:Deglr6328

https://commons.wikimedia.org/wiki/File:Fluorescent_lighting_spectrum_peaks_labelled.png
Peak numberWavelength of peak (nm)Species producing peakActual line location (nm)
1405.4mercury404.656
2436.6mercury435.833
3487.7terbium from Tb3+~485 to 490
4542.4terbium from Tb3+~543 to 544
5546.5mercury546.074
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

Astro: http://www.threehillsobservatory.co.uk/astro/spectroscopy.htm

Hg Lines: http://www.astrosurf.com/buil/us/spe2/hresol4.htm

Hg Lines:

Wavelength (nm)Name (see photoresist)Color
184.45 ultraviolet (UVC)
253.7 ultraviolet (UVC)
365.4I-lineultraviolet (UVA)
404.7H-lineviolet
435.8G-lineblue
546.1 green
578.2 yellow-orange


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