{"id":7034,"date":"2023-07-29T06:44:45","date_gmt":"2023-07-29T06:44:45","guid":{"rendered":"https:\/\/41j.com\/blog\/?p=7034"},"modified":"2023-07-29T06:44:45","modified_gmt":"2023-07-29T06:44:45","slug":"random-notes-5","status":"publish","type":"post","link":"https:\/\/41j.com\/blog\/2023\/07\/random-notes-5\/","title":{"rendered":"Random Notes 5"},"content":{"rendered":"\n

Xaar 128

<\/p>\n\n\n\n

https:\/\/github.com\/MatthiasWM\/Xaar128<\/a><\/p>\n\n\n\n

https:\/\/github.com\/gkyle\/xaar128<\/a><\/p>\n\n\n\n

https:\/\/www.xaar.com\/en\/products\/xaar-printheads\/xaar-128\/<\/a><\/p>\n\n\n\n

http:\/\/ytec3d.com\/forum\/viewtopic.php?t=47<\/a><\/p>\n\n\n\n

chinese inkjet info: http:\/\/m.6lon.com\/sdm\/132165\/2\/cp-1003311\/0.html<\/a><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

RNA Bioanalyzer

<\/p>\n\n\n\n

Paper<\/td>Quantification pg\/ul RNA<\/td>Run<\/td>Plots<\/td><\/tr>
Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols<\/a><\/td>397.5 ng\/60 mL (Qubit RNA HS)<\/td>Agilent 4200 TapeStationRIN: 5.9<\/td>\"An<\/td><\/tr>
Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols<\/a><\/td>397.5 ng\/60 mL(Qubit RNA HS)<\/td>Agilent 4200 TapeStationRIN: 3.3<\/td>\"An<\/td><\/tr>
Deep Sequencing of Urinary RNAs for Bladder Cancer Molecular Diagnostics<\/a><\/td>0.98 ng\/mL0.08 ng\/mLProcessed within two hours of collection<\/td>Agilent 2100 Bioanalyzer, RNA Pico chipsRIN ranged from 2.5 to 9.5Mean: 6.03<\/td>No plots<\/td><\/tr>
Identification of microRNAs in blood and urine as tumour markers for the detection of urinary bladder cancer<\/a><\/td>~2 ng\/uL (fig. 1)<\/td>Several urine RNA isolates showed low RIN values <3<\/td>No plots<\/td><\/tr>
Urinary MicroRNA-Based Diagnostic Model for Central Nervous System Tumors Using Nanowire Scaffolds<\/a><\/td>Qubit microRNA Assay<\/td>Agilent 2100 BioanalyzerRIN: 8<\/td>\"1638356162683-129.png\"<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

RNA Papers

<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n

SingleMol Imaging

<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n

Solid state Nanopore

Hitachi, making pores with dialectric breakdown, slowing, notes on viscosity to slow etc:\u00a0https:\/\/www.nature.com\/articles\/srep31324.pdf<\/a>

<\/p>\n\n\n\n

Keio University group, optical observation of translocation: https:\/\/iopscience.iop.org\/article\/10.7567\/APEX.9.017001\/pdf<\/a><\/p>\n\n\n\n


Amplification\/Electronics

<\/h2>\n\n\n\n

ASIC Design, to go to 1MHz: https:\/\/www.nature.com\/articles\/nmeth.1932<\/a><\/p>\n\n\n\n

Noise measurements from above:

<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

Instrumentation for Low-Noise High-Bandwidth Nanopore Recording. Engineered Nanopores for Bioanalytical Applications: <\/em>https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9781437734737000030<\/a><\/p>\n\n\n\n

Above has lots of nice protocol information.<\/p>\n\n\n\n

Ionic Speed\/Current<\/h4>\n\n\n\n

“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 <\/sup>Coulombs (that is 1 electron or 1 proton charge), then we see that a current of about one pA corresponds to roughly 107<\/sup> 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\/<\/a><\/p>\n\n\n\n

Molecular Dynamics of Ionic Current:\u00a0https:\/\/www.ks.uiuc.edu\/Research\/silica\/IonRect.html<\/a>

<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

DNA Speed:
From, measures time to translocate two adjacent pores. distance is ~1.5um:\u00a0https:\/\/pubs.acs.org\/doi\/full\/10.1021\/nl2030079<\/a>

<\/h2>\n\n\n\n
\"\"<\/figure>\n\n\n\n

Folded\/Knotted DNA:
<\/h2>\n\n\n\n

Detection of knotted DNA<\/p>\n\n\n\n

https:\/\/www.nature.com\/articles\/nnano.2016.153<\/a><\/p>\n\n\n\n

https:\/\/www.nature.com\/articles\/s41467-019-12358-4<\/a><\/p>\n\n\n\n

Folding<\/p>\n\n\n\n

https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/20608744<\/a><\/p>\n\n\n\n

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.<\/p>\n\n\n\n

\nhttps:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.nanolett.8b04715\n<\/div><\/figure>\n\n\n\n

Hairpins, P2000 pulled quartz nano-pipette. Using hairpins to encode DNA 8bp and 16bp hairpins.<\/p>\n\n\n\n

DNA Folds for data storage by Ulrich: https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/30585490<\/a><\/p>\n\n\n\n


<\/a><\/h2>\n","protected":false},"excerpt":{"rendered":"

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 Paper Quantification pg\/ul RNA Run Plots Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols 397.5 ng\/60 mL (Qubit RNA HS) Agilent 4200 TapeStationRIN: 5.9 Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols 397.5 ng\/60 mL(Qubit RNA HS) Agilent […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-7034","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p1RRoU-1Ps","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/7034","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/comments?post=7034"}],"version-history":[{"count":1,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/7034\/revisions"}],"predecessor-version":[{"id":7050,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/7034\/revisions\/7050"}],"wp:attachment":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/media?parent=7034"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/categories?post=7034"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/tags?post=7034"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}