I-10x Genomics Visium Spatial Transcriptome
Izici
● Ukulungiswa: 100 µM
● Ububanzi be-Spot: 55 µM
● Inombolo yezindawo: 4992
● Indawo yokuthwebula: 6.5 x 6.5 mm
● Indawo ngayinye enebhakhodi ilayishwa ama-primers akhiwe izigaba ezi-4:
- umsila we-poly(dT) we-mRNA priming kanye ne-cDNA synthesis
- I-Unique Molecular Identifier (UMI) ukulungisa ukuchema kokukhulisa
- Ibhakhodi yendawo
- Ukulandelana okubophezelayo kokufunda ingxenye yokuqala yokulandelana engu-1
● Ukungcoliswa kwe-H&E kwezigaba
Izinzuzo
●Isevisi yokuma okukodwa: ihlanganisa konke okuhlangenwe nakho nezinyathelo ezisekelwe emakhono, okuhlanganisa ukuhlukanisa i-cryo, ukungcolisa, ukwenza kahle kwezicubu, ukufaka ibhakhodi yendawo, ukulungiswa komtapo wolwazi, ukulandelana kanye ne-bioinformatics .
● Ithimba lobuchwepheshe elinamakhono aphezulu: onolwazi ngezinhlobo zezicubu ezingaphezu kuka-250 nezinhlobo eziyi-100+ ezihlanganisa abantu, igundane, izilwane ezincelisayo, izinhlanzi nezitshalo.
●Isibuyekezo sesikhathi sangempela kuyo yonke iphrojekthi: ngokulawula okugcwele kokuqhubeka kokuhlolwa.
●I-bioinformatics ejwayelekile ejwayelekile:Iphakethe lihlanganisa ukuhlaziya okungu-29 kanye nezibalo ezisezingeni eliphakeme eziyi-100+.
●Ukuhlaziywa kwedatha okwenziwe ngendlela oyifisayo nokubona ngeso lengqondo: itholakalela izicelo zocwaningo ezahlukene.
●Ukuhlaziya okuhlangene ongakukhetha nokulandelana kwe-Single-cell mRNA
Imininingwane
| Izidingo Zesampula | Umtapowolwazi | Isu lokulandelanisa | Idatha iyanconywa | Ikhwalithi yokulawula |
| Amasampula e-cryo ashumekwe OCT, amasampuli e-FFPE (Ubukhulu obukhulu: cishe 6x6x6 mm3) 3 amabhlogo isampula ngayinye | Ilabhulali ye-10X Visium cDNA | I-Ilumina PE150 | 50K PE ifundwa indawo ngayinye (60Gb) | I-RIN>7 |
Ukuze uthole imininingwane eyengeziwe ngomhlahlandlela wokulungiselela isampula kanye nokuhamba komsebenzi wesevisi, sicela ukhululeke ukukhuluma no-aUchwepheshe we-BMKGENE
Uhlelo lokusebenza lwesevisi
Esigabeni sokulungiselela isampula, uhlolo lokuqala lwenqwaba ye-RNA lwenziwa ukuze kuqinisekiswe ukuthi i-RNA yekhwalithi ephezulu ingatholakala.Esigabeni sokuthuthukisa izicubu izigaba ziba namabala futhi zibonwa ngeso lengqondo futhi nezimo ze-permeabilization zokukhululwa kwe-mRNA ezicutshini ziyathuthukiswa.Iphrothokholi elungiselelwe ibe isisetshenziswa phakathi nokwakhiwa komtapo wolwazi, kulandelwa ukulandelana nokuhlaziya idatha.
Ukugeleza komsebenzi okuphelele kwesevisi kuhilela izibuyekezo zesikhathi sangempela neziqinisekiso zeklayenti ukuze kugcinwe iluphu yempendulo ephendulayo, okuqinisekisa ukwenziwa kwephrojekthi okushelelayo.
Kufaka ukuhlaziya okulandelayo:
Ukulawulwa Kwekhwalithi Yedatha:
o Ukukhishwa kwedatha kanye nokusatshalaliswa kwamaphuzu ekhwalithi
o Ukutholwa kofuzo endaweni ngayinye
o Ukumbozwa kwezicubu
Ukuhlaziywa kwesampula yangaphakathi:
o Ukunotha kofuzo
o Ukuhlanganisa amabala, okuhlanganisa ukuhlaziywa kobukhulu obuncishisiwe
o Ukuhlaziywa kwenkulumo ehlukile phakathi kwamaqoqo: ukuhlonza izakhi zofuzo zomaka
o Isichasiselo esisebenzayo kanye nokunothiswa kwezakhi zofuzo zomaka
Ukuhlaziya kwamaqembu
o Ukuhlanganiswa kabusha kwamachashaza kuwo womabili amasampula (isib. aphethwe yisifo nokulawula) kanye nokuhlanganisa kabusha
o Ukuhlonza izakhi zofuzo zomaka zeqoqo ngalinye
o Isichasiselo esisebenzayo kanye nokunothiswa kwezakhi zofuzo zomaka
o Ukuvezwa Okuhlukile kweqoqo elifanayo phakathi kwamaqembu
Ukuhlaziywa kwesampula yangaphakathi
Ukuhlanganisa amabala
Ukuhlonza izakhi zofuzo zomaka kanye nokusabalalisa kwendawo
Inter-group Analysis
Inhlanganisela yedatha kusuka womabili amaqembu kanye neqoqo kabusha
Izakhi zofuzo zomaka zamaqoqo amasha
Hlola intuthuko egqugquzelwa isevisi ye-BMKGene yokubhala ngezindawo nge-10X Visium Kulezi zincwadi ezifakiwe:
Chen, D. et al.(2023) 'mthl1, i-Drosophila homologue engaba khona ye-GPCRs yokunamathela kwezilwane ezincelisayo, ibandakanyeka ekuphenduleni kwe-antitumor kumaseli afakwe i-oncogenic ezimpukaneni', Proceedings of the National Academy of Sciences of the United States of America, 120(30), p.e2303462120.doi: /10.1073/pnas.2303462120
Chen, Y. et al.(2023) 'I-STEEL inika amandla ukucaciswa kokulungiswa okuphezulu kwedatha ye-spatiotemporal transcriptomic', Briefings in Bioinformatics, 24(2), pp. 1–10.doi: 10.1093/BIB/BBAD068.
U-Liu, C. et al.(2022) 'I-atlas ye-spatiotemporal ye-organogenesis ekuthuthukisweni kwezimbali ze-orchid', Nucleic Acids Research, 50(17), pp. 9724-9737.doi: 10.1093/NAR/GKAC773.
Wang, J. et al.(2023) 'Ukuhlanganisa I-Spatial Transcriptomics kanye ne-Single-nucleus RNA Sequencing Yembula Amaqhinga Angaba Khona Okwelapha E-Uterine Leiomyoma', Ijenali Yamazwe Ngamazwe Yesayensi Yezinto Eziphilayo, 19(8), pp. 2515–2530.doi: 10.7150/IJBS.83510.
