I-10x Genomics Visium Spatial Transcriptome
Inkqubo yoBugcisa
Iimbonakalo
● Isisombululo: 100 µM
● Ububanzi bebala: 55 µM
● Inani leendawo: 4992
● Indawo yokubamba: 6.5 x 6.5 mm
● Indawo nganye enebhakhowudi igcwele iiprimer ezenziwe ngamacandelo ama-4:
- umsila we-poly(dT) wokulungiselela i-mRNA priming kunye nokwenziwa kwe-cDNA
- I-Unique Molecular Identifier (UMI) yokulungisa i-amplification bias
- Ibhakhodi yendawo
- Ulandelelwano lokubopha lweprimer yokulandelelana yokufunda okuyingxenye 1
● Ukupenda iindawo nge-H&E
Iingenelo
●Inkonzo yokumisa yonke indawo: idibanisa onke amanyathelo asekelwe kumava kunye nezakhono, kuquka ukuqhekeza i-cryo, ukudaya, ukuphucula izicubu, ukubhalwa kwebarcode kwindawo, ukulungiswa kwethala leencwadi, ukulandelelana kunye ne-bioinformatics.
● Iqela lobuchwephesha elinobuchule obuphezulu: unamava kwiintlobo zezicubu ezingaphezu kwama-250 kunye neentlobo ezingaphezu kwe-100 kuquka abantu, impuku, izilwanyana ezincancisayo, iintlanzi kunye nezityalo.
●Uhlaziyo lwexesha langempela kwiProjekthi yonke: ngolawulo olupheleleyo lwenkqubela phambili yovavanyo.
●I-Bioinformatics eQhelekileyo eBanzi:Iphakheji ibandakanya uhlalutyo olungama-29 kunye namanani angaphezulu kwe-100 asemgangathweni ophezulu.
●Uhlalutyo lweDatha oluCwangcisiweyo kunye nokuBonakala: iyafumaneka kwizicelo ezahlukeneyo zophando.
●Uhlalutyo oluDibeneyo oluKhethekileyo oluneSilingi se-mRNA esinye
Iinkcukacha
| Iimfuno zeSampuli | Ithala leeNcwadi | Icebo lokulandelelanisa izinto | Idatha iyacetyiswa | Ulawulo lwemeko |
| Iisampulu ze-cryo ezifakwe kwi-OCT (Ububanzi obufanelekileyo: malunga ne-6x6x6 mm³) Iibhloko ezi-2 kwisampulu nganye | Ithala leencwadi le-10X Visium cDNA | I-Illumina PE150 | Ukufundwa kwe-50K PE kwindawo nganye (60Gb) | I-RIN > 7 |
Ukuze ufumane iinkcukacha ezithe vetshe malunga nesikhokelo sokulungiselela isampuli kunye nendlela yokusebenza kwenkonzo, nceda uzive ukhululekile ukuthetha nomntuIngcali ye-BMKGENE
Ukuhamba komsebenzi wenkonzo
Kwisigaba sokulungiselela isampuli, uvavanyo lokuqala lokukhupha i-RNA eninzi luyenziwa ukuqinisekisa ukuba i-RNA esemgangathweni ophezulu inokufunyanwa. Kwisigaba sokuphucula izicubu, amacandelo ayadayazwa kwaye abonwe kwaye iimeko zokungena kwe-mRNA kwizicubu ziyaphuculwa. Iprotokholi ephuculiweyo emva koko isetyenziswa ngexesha lokwakhiwa kwethala leencwadi, kulandele ulandelelwano kunye nohlalutyo lwedatha.
Umsebenzi opheleleyo wenkonzo ubandakanya uhlaziyo lwangempela kunye nokuqinisekiswa kwabathengi ukugcina i-feedback loop ephendulayo, ukuqinisekisa ukuphunyezwa kweprojekthi okuhamba kakuhle.
Kubandakanya uhlalutyo olulandelayo:
Ulawulo loMgangatho weDatha:
o Ukusasazwa kwedatha kunye nomgangatho wamanqaku
o Ukufunyanwa kwezakhi zofuzo kwindawo nganye
o Ukugqunywa kwezicubu
Uhlalutyo lwesampulu yangaphakathi:
o Ukutyeba kwezakhi zofuzo
o Ukuqokelelana kwamabala, kuquka uhlalutyo lobukhulu obuncitshisiweyo
o Uhlalutyo lokubonakaliswa komahluko phakathi kwamaqela: ukuchongwa kwezakhi zofuzo eziphawulayo
o Inkcazo esebenzayo kunye nokutyebisa iijini zophawu
Uhlalutyo lwamaqela ahlukeneyo
o Ukudibanisa kwakhona amabala avela kwiisampuli zombini (umz. ezinesifo kunye nezilawulwayo) kunye nokudibanisa kwakhona
o Ukuchongwa kwezakhi zofuzo zeqela ngalinye
o Inkcazo esebenzayo kunye nokutyebisa iijini zophawu
o Ukubonakaliswa kokwahluka kweqela elifanayo phakathi kwamaqela
Uhlalutyo lwesampulu yangaphakathi
Ukuqokelelana kwamabala
Ukuchongwa kwezakhi zofuzo eziphawulayo kunye nokusasazwa kwendawo
Uhlalutyo lwamaqela ahlukeneyo
Indibaniselwano yedatha evela kumaqela omabini kunye ne-re-cluster
Iimpawu ze-marker ze-clusters ezintsha
Hlola inkqubela phambili eyenziwe yinkonzo ye-BMKGene's spatial transcriptomics yi-10X Visium. Kule mibhalo iphambili:
UChen, D. et al. (2023) 'mthl1, into efana neDrosophila enokuba yi-GPCRs yokunamathela kwezilwanyana ezincancisayo, ibandakanyeka kwiimpendulo zokulwa nomhlaza kwiiseli ezifakwe kwi-oncogenic kwiimpukane',Iingxelo zeNational Academy of Sciences yaseUnited States of America, 120(30), p. e2303462120. doi: /10.1073/pnas.2303462120
UChen, Y. et al. (2023) 'I-STEEL ivumela ukucaciswa okuphezulu kwedatha ye-spatiotemporal transcriptomic',Iingxelo-nkcazelo kwi-Bioinformatics, 24(2), iphepha 1–10. doi: 10.1093/BIB/BBAD068.
ULiu, C. et al. (2022) 'I-atlas yendawo ye-organogenesis ekuphuhlisweni kweentyatyambo ze-orchid',Uphando lweNucleic Acids, 50(17), iphepha 9724-9737. doi: 10.1093/NAR/GKAC773.
UWang, J. et al. (2023) 'Ukudibanisa iSpatial Transcriptomics kunye neSingle-nucleus RNA Sequencing Kutyhila Amaqhinga Onyango Anokubakho kwi-Uterine Leiomyoma',Ijenali yeHlabathi yeSayensi yeBiological, 19(8), iphepha 2515–2530. doi: 10.7150/IJBS.83510.
