I-10x ye-Genomics yeVisium ye-Spatial Transcriptome
Iimbonakalo
● Isisombululo: 100 µM
● I-Spot Diameter: 55 µM
● Inani lamabala: 4992
● Indawo yokubamba: 6.5 x 6.5 mm
● Indawo nganye enebhakhowudi ilayishwe ngeziqalo ezenziwe ngamacandelo ama-4:
-Ipoly(dT) umsila we-mRNA priming kunye ne-cDNA synthesis
-I-Unique Molecular Identifier (UMI) ukulungisa i-aplification bias
-Ibhakhowudi yendawo
- Ulandelelwano olubophelelayo lokufunda ngokuyinxenye 1 i-primer elandelelanayo
● Ukungcoliswa kwe-H&E yamacandelo
Iingenelo
●Inkonzo yokumisa enye: idibanisa onke amava kunye namanyathelo asekelwe kwizakhono, kuquka i-cryo-sectioning, i-staining, i-tissue optimization, i-barcoding yendawo, ukulungiswa kwethala leencwadi, ulandelelwano kunye ne-bioinformatics.
● Iqela lobugcisa elinobuchule obuphezulu: onamava ngaphezu kwe-250 yeentlobo zeethishu kunye ne-100+ yeentlobo ezibandakanya abantu, impuku, isilwanyana esanyisayo, intlanzi kunye nezityalo.
●Uhlaziyo lwexesha lokwenyani kuyo yonke iprojekthi: ngolawulo olupheleleyo lwenkqubela phambili yovavanyo.
●Umgangatho obanzi we-bioinformatics:iphakheji ibandakanya 29 uhlalutyo kunye 100+ amanani aphezulu.
●Uhlalutyo lwedatha eyenziwe ngokwezifiso kunye nokubonwa: iyafumaneka kwizicelo ezahlukeneyo zophando.
●Uhlalutyo oludityanisiweyo ngokuzikhethela kunye nolandelelwano lwe-mRNA yeseli enye
Iinkcukacha
| IiMfuno zeSampulu | Ithala leencwadi | Isicwangciso sokulandelelana | Idatha iyacetyiswa | Ulawulo lwemeko |
| Iisampuli ze-cryo ezifakwe kwi-OCT, iisampuli ze-FFPE (Elona dayamitha ilungileyo: malunga ne-6x6x6 mm3) Iibhloko ezi-3 kwisampuli nganye | Ithala leencwadi le-10X Visium cDNA | Illumina PE150 | I-50K PE ifundeka kwindawo nganye ( 60Gb ) | I-RIN>7 |
Ukufumana iinkcukacha ezithe vetshe malunga nesikhokelo sokulungiselela isampula kunye nokuhamba komsebenzi wenkonzo, nceda uzive ukhululekile ukuthetha nayeBMKGENE ingcaphephe
Ukuhanjiswa kwenkonzo
Kwinqanaba lolungiselelo lwesampulu, ulingo lokuqala lwe-RNA yesixa esikhulu lwenziwa ukuqinisekisa ukuba i-RNA yomgangatho ophezulu inokufumaneka.Kwinqanaba lokuphucula izicubu amacandelo abonakaliswe kwaye abonakaliswe kwaye iimeko ze-permeabilization zokukhululwa kwe-mRNA kwiithishu ziphuculwe.Iprothokholi ephuculweyo isetyenziswa ngexesha lolwakhiwo lwethala leencwadi, ilandelwa lulandelelwano kunye nohlalutyo lwedatha.
Inkonzo epheleleyo yokuhamba komsebenzi ibandakanya uhlaziyo lwexesha langempela kunye neziqinisekiso zabaxumi ukugcina i-loop yempendulo ephendulayo, ukuqinisekisa ukuphunyezwa kweprojekthi kakuhle.
Ibandakanya uhlalutyo olulandelayo:
Ulawulo Lomgangatho Wedatha:
o Isiphumo sedatha kunye nokuhanjiswa kwamanqaku asemgangathweni
o Ukufunyanwa kwemfuza kwindawo nganye
o Ukugquma kwezicubu
Uhlalutyo lwesampulu yangaphakathi:
o Ubutyebi bemfuza
o Ukuhlanganiswa kwamabala, kubandakanywa uhlalutyo oluncitshisiweyo lobungakanani
o Uhlalutyo lwentetho eyohlukileyo phakathi kwamaqela: ukuchongwa kofuzo lokumakisha
o Inkcazo esebenzayo kunye nokutyetyiswa kweejene zokumakisha
Uhlalutyo lwamaqela
o Ukudityaniswa kwakhona kwamabala kuzo zombini iisampulu (umzekelo, izifo kunye nolawulo) kunye nokuphinda kuhlangane
o Ukuchongwa kofuzo olumakishayo kwiqela ngalinye
o Inkcazo esebenzayo kunye nokutyetyiswa kweejene zokumakisha
o Umahluko Ubonakaliso lweqela elifanayo phakathi kwamaqela
Uhlalutyo lwesampulu yangaphakathi
Ukuhlanganiswa kwamabala
Ukuchongwa kofuzo lophawu kunye nokuhanjiswa kwendawo
Uhlalutyo lwamaqela
Indibaniselwano yedatha esuka kumaqela omabini kunye neqela kwakhona
Iijeni zokumakisha zamaqela amatsha
Phonononga inkqubela phambili eququzelelwa yinkonzo ye-BMKGene ye-spatial transcriptomics ngo-10X Visium Kolu papasho lubonakalisiweyo:
Chen, D. et al.(2023) 'mthl1, i-Drosophila homologue enokubakho ye-mammalian adhesion GPCRs, ibandakanyeka kwiimpendulo ze-antitumor kwiiseli ze-oncogenic ezifakwe kwiimpukane', Iinkqubo ze-National Academy of Sciences yase-United States yaseMelika, i-120 (30), iphe.e2303462120.doi: /10.1073/pnas.2303462120
Chen, Y. et al.(2023) 'I-STEEL yenza i-high-resolution delineation yedatha ye-spatiotemporal transcriptomic', Iinkcazo kwi-Bioinformatics, i-24 (2), iphe. 1-10.doi: 10.1093/BIB/BBAD068.
U-Liu, uC. et al.(2022) 'I-atlas ye-spatiotemporal ye-organogenesis ekuphuhlisweni kweentyatyambo ze-orchid', Uphando lwe-Nucleic Acids, i-50 (17), iphe. 9724-9737.doi: 10.1093/NAR/GKAC773.
Wang, J. et al.(2023) 'Ukudibanisa i-Spatial Transcriptomics kunye ne-Single-nucleus ye-RNA Sequencing ityhila iiNdlela eziNgcono zonyango lwe-Uterine Leiomyoma', i-International Journal ye-Biological Sciences, i-19 (8), iphepha 2515-2530.doi: 10.7150/IJBS.83510.
