Ukulandelana Okuphelele Kwe-Transcriptome - Illumina
Izici
● Ukwakhiwa kwelabhulali okubili ukuze kulandelwe i-transcriptome ephelele: umtapo wolwazi wokuncipha kwe-rRNA kanye nokulungiswa komtapo wolwazi we-RNA encane.
● Ukuhlaziywa okuphelele kwe-bioinformatic kwe-mRNA, i-lncRNA, i-circRNA kanye ne-miRNA emibikweni ehlukanisiwe ye-bioinformatic, kanye nokuhlaziywa okuhlangene nakho konke ukubonakaliswa kwe-RNA kuhlanganisiwe, kufaka phakathi ukuhlaziywa kwamanethiwekhi e-ceRNA.
Izinzuzo Zesevisi
●Ubuchwepheshe Obubanzi: Sicubungule amaphrojekthi angaphezu kuka-2100 aphelele e-transcriptome, ahlanganisa izinhlobo ezahlukene zamasampula. Siletha ingcebo yobuchwepheshe kuyo yonke iphrojekthi.
●Ukulawulwa Kwekhwalithi Okuqinile: Sisebenzisa amaphuzu okulawula ayisisekelo kuzo zonke izigaba, kusukela ekulungiseleleni amasampula kuya ekulungiseleleni umtapo wolwazi, ukulandelana kanye ne-bioinformatics. Ukuqapha kwethu ngokucophelela kuqinisekisa ukulethwa kwemiphumela esezingeni eliphezulu njalo.
●Isichasiselo Esiphelele: Sisebenzisa izizindalwazi eziningi ukuze sichaze ngokusebenza i-Differentially Expressed Genes (DEGs) futhi senze ukuhlaziywa kokunotha okuhambisanayo. Le ndlela ebanzi inikeza ukuqonda ngezinqubo zamaseli kanye nama-molecule ezisekela impendulo ye-transcriptome, okuqinisekisa ukuthi uthola lonke ulwazi olungenzeka mayelana nedatha yokuhlolwa kwakho.
●Ukuhlaziywa Okujulile Kwezinethiwekhi Zokulawula: ukuhlaziywa kwenethiwekhi ye-ceRNA kuvunyelwe ngokulandelana okuhlangene kwe-mRNA, i-lncRNA, i-circRNA, ne-miRNA kanye nomsebenzi ophelele we-bioinformatic.
●Usekelo Lwangemva Kokuthengisa: Siyaqonda ukuthi kubaluleke kangakanani ukuba khona, yingakho ukuzibophezela kwethu kudlulela ngale kokuphothulwa kwephrojekthi ngesikhathi senkonzo yezinyanga ezintathu ngemuva kokuthengisa. Phakathi nalesi sikhathi, sinikeza ukulandelwa kwephrojekthi, usizo lokuxazulula izinkinga, kanye nezikhathi ze-Q&A ukuze kuxazululwe noma yimiphi imibuzo ehlobene nemiphumela.
Izidingo Zesampula Nokulethwa
| Umtapo Wolwazi | Isu lokulandelana kwezigaba | Kunconywa idatha | Ikhwalithi yokulawula |
| i-rRNA inciphile | I-Illumina PE150 | 16 Gb | Q30≥85% |
| Usayizi ukhethiwe | I-Illumina SE50 | Ukufundwa okungu-10-20M |
Izidingo Zesampula:
Ama-Nucleotide:
| I-Conc.(ng/μl) | Inani (μg) | Ubumsulwa | Ubuqotho |
| ≥ 80 | ≥ 1.6 | OD260/280=1.7-2.5 OD260/230=0.5-2.5 Ukungcoliswa kwephrotheni noma i-DNA okulinganiselwe noma okungekho nhlobo kukhonjisiwe kujeli. | I-RIN≥6.0 5.0≥28S/18S≥1.0; ukuphakama okulinganiselwe noma okungekho kwesisekelo |
Ukulethwa Kwesampula Okunconyiwe
Isitsha: Ishubhu le-centrifuge elingu-2 ml (Akukhuthazwa ukusebenzisa i-tin foil)
Ukulebula kwesampula: Iqembu + ukukopisha isib. A1, A2, A3; B1, B2, B3.
Ukuthunyelwa:
1. Iqhwa elomile: Amasampula kudingeka apakishwe ezikhwameni bese egqitshwa eqhweni elomile.
2. Amashubhu e-RNAstable: Amasampula e-RNA angomiswa eshubhu lokuzinzisa i-RNA (isb. i-RNAstable®) bese ethunyelwa ekushiseni kwegumbi.
Ukugeleza Komsebenzi Wesevisi
Umklamo wokuhlola
Ukulethwa kwesampula
Ukukhishwa kwe-RNA
Ukwakhiwa komtapo wolwazi
Ukulandelana
Ukuhlaziywa kwedatha
Izinsizakalo zangemuva kokuthengisa
I-Bioinformatics
Ngaphezu kwakho konke ukuhlaziywa kwezinhlobo ezine ze-RNA ezihlukile, izinhlobo ezine ze-RNA zihlanganiswe ekuhlaziyweni kwethu okuhlangene:
- Ukuhlaziywa kokubonakaliswa ngokubambisana phakathi kwazo zonke izinhlobo ezahlukene zedatha ye-RNA
- Ukubuka konke kokubonakaliswa kwe-RNA
- Ukubuka konke kokubonakaliswa kokwehluka
- Inethiwekhi ye-CeRNA
- Izakhi zofuzo ezibalulekile ezihlanganisiwe endleleni
- Ukuhlaziywa kokulondolozwa kwemvelo
- Ubudlelwano obuqondisiwe
Ukubuka konke kokubonakaliswa kwe-RNA
Izakhi zofuzo ezivezwe ngokuhlukile
ukuhlaziywa kwe-ceRNA
Ama-miRNA ahlukaniswe ngokuhlukile kanye nama-RNA ahlobene
Hlola intuthuko yocwaningo eyenziwe yizinsizakalo zokulandelana kwezincwadi ze-BMKGene ngokusebenzisa iqoqo lezincwadi ezikhethiwe.
UDai, Y. et al. (2022) 'Amaphrofayili okubonakaliswa okuphelele kwama-mRNA, ama-lncRNA nama-miRNA esifweni sikaKashin-Beck ahlonzwe ngokulandelana kwe-RNA',Ama-Molecular Omics, 18(2), amakhasi 154-166. doi: 10.1039/D1MO00370D.
ULiu, N. nan nabanye. (2022) 'Ukuhlaziywa kwe-transcriptomes ephelele yokumelana nokubanda kwe-Apis cerana eNtabeni iChangbai ngesikhathi sobusika.',I-Gene, 830, amakhasi 146503–146503. doi: 10.1016/J.GENE.2022.146503.
UWang, XJ nabanye. (2022) 'Ukubekwa phambili okusekelwe ekuhlanganisweni kwe-Multi-Omics kwamanethiwekhi okulawula i-RNA ancintisanayo kumdlavuza wamaphaphu wamangqamuzana amancane: izici zama-molecular kanye nabantu abazosebenzisa izidakamizwa',Imingcele ku-Oncology, 12, ikhasi. 904865. doi: 10.3389/FONC.2022.904865/BIBTEX.
Xu, P. et al. (2022) 'Ukuhlaziywa okuhlanganisiwe kwamaphrofayili okubonakaliswa kwe-lncRNA/circRNA-miRNA-mRNA kwembula ukuqonda okusha ngezindlela ezingaba khona ekuphenduleni ama-nematode e-root-knot kuma-peanut',I-BMC Genomics, 23(1), amakhasi 1–12. doi: 10.1186/S12864-022-08470-3/FIGURES/7.
UYan, Z. et al. (2022) 'Ukulandelana kwe-RNA ebhalwe ngokuphelele kugqamisa izindlela zama-molecule ezihlotshaniswa nokugcinwa kwekhwalithi yangemva kokuvunwa ku-broccoli ngemisebe ebomvu ye-LED',Ibhayoloji kanye nobuchwepheshe ngemva kokuvuna, 188, ikhasi 111878. doi: 10.1016/J.POSTHARIVBIO.2022.111878.
