I-Assay ye-Chromatin eFikelelekayo yeTransposase kunye noSetyenziso lwe-High throughput (ATAC-seq)
Iimpawu zeNkonzo
● Inkonzo ifuna iisampulu zethishu, endaweni yee-nucleic acids ezitsaliweyo, ukulondoloza ukudibana kwe-DNA-protein.
● Indlela ye-ATAC ibandakanya ukuchithwa kwezicubu, ilandelwa yi-nuclei isolation, unyango lwe-Tn5 kunye nokuhlanjululwa, ukukhulisa i-PCR, ukukhethwa kobukhulu kunye nokulandelelana.
● Ulandelelwano kwi-Illumina NovaSeq
Iinkonzo eziluncedo
●Uvakalelo oluPhezulu:ubungakanani beseli yokuqala esezantsi yanele ukulungiselela ithala leencwadi kunye nolandelelwano.
●Ubuchwephesha obunolwazi oluphezulu: ngaxeshanye ityhila iindawo ze-genomic zechromatin evulekileyo kunye nezinto ezisebenzayo zolawulo ezifana ne-transcription factor binding sites.
●UVeliso oluLungileyo loMfuniselo: iikopi zobugcisa zibonisa ukuphindaphinda okugqwesileyo.
●UbuGcisa obuBanzi: kunye namakhulu eeprojekthi zolandelelwano ze-ATAC ezigqitywe ngempumelelo, i-BMKGENE izisa ngaphezulu kweminyaka elishumi yamava, iqela lokuhlalutya abanobuchule obuphezulu, umxholo obanzi, kunye nenkxaso egqwesileyo emva kokuthengisa.
●Ukubanakho ukujoyina kunye nohlalutyo lwe-Transcriptomics: ukuvumela uhlalutyo oludibeneyo lwe-ATAC seq kunye nezinye iinkcukacha ze-omics ezifana ne-RNA-seq.
● Uhlalutyo oluBanzi lwe-Bioinformatic: ukwenza ukuba kungekuphela ukuchongwa kwemimandla evulekileyo ye-chromatin kunye nokusebenza kwayo okuhambelanayo (abagqugquzeli, i-UTs, i-exons, i-introns) kodwa kunye nohlalutyo lwamahluko phakathi kwemimandla evulekile ye-chromatin phakathi kweesampuli.
IiNgcaciso zeNkonzo
| Ithala leencwadi | Isicwangciso solandelelwano | Imveliso yedatha ecetyiswayo | Ulawulo lwemeko |
| I-ATAC-seq | Illumina PE150 | > 20M iyafundwa Kuxhomekeke kubungakanani begenome (Umntu: 50 M iyafunda) | Q30≥85% |
IiMfuno zeSampulu
Uhlobo lweesampulu: Izicubu, iiseli eziphilayo okanye engumkhenkce, igazi
● Inombolo yeSeli: ≥ 106iiseli
● Ubunzima bezicubu: ≥ 200mg izicubu ezitsha
● Igazi: ≥ 4 mL
Ukuhamba komsebenzi weNkonzo
Uyilo lovavanyo
Ukuhanjiswa kwesampuli
Ukutsalwa kwe-DNA
Ukwakhiwa kwethala leencwadi
Ukulandelelanisa
Uhlalutyo lwedatha
Iinkonzo emva kokuthengisa
Ibandakanya uHlahlelo Olulandelayo:
● Ulawulo lomgangatho wedatha ekrwada;
● Incopho yobizo olusekwe kwimephu yegenome;
● Inkcazo yemfuza kwindawo encopho;
● Uhlalutyo lwe-Motif: ukuchongwa kweendawo ezibophelelayo ze-transcription factor (TFBS);
● Uhlalutyo lweNcopho eyahlukileyo kunye nenkcazo.
I-1.I-Heatmap kwi-ATAC ifundeka ngokusasazwa kwi-TSS nakwimimandla ekufutshane (±3 kb)
2.Ukusasazwa kwendawo evulekileyo yechromatin kumacandelo ahlukeneyo ejenome
3.Incopho yokufowuna phakathi kwamaqela
Phonononga inkqubela phambili yophando eququzelelwa yi-BMKGene ye-ATAC yeenkonzo zolandelelwano ngengqokelela egciniweyo yopapasho.
Fu, A.okqhubekayo.(2023) 'i-Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) ibonisa uphuhliso lweziqhamo, ukwakheka kunye nokuvuthwa kweempawu zemfuzo',Uphando lweHorticulture, 10(1). doi: 10.1093/HR/UHAC228.
Gonga, B.okqhubekayo.(2023) 'I-Epigenetic kunye ne-transcriptal activation ye-secretory kinase FAM20C njenge-oncogene kwi-glioma',Ijenali yeGenetics kunye neGenomics, 50(6), iphepha 422–433. doi: 10.1016/J.JGG.2023.01.008.
Yena, Y.okqhubekayo.(2023) 'I-Butyrate ibuyisela umva ukunganyangeki kwe-ferroptosis kumhlaza we-colorectal ngokunyanzelisa ukucinezelwa kwe-c-Fos-exhomekeke kwi-xCT',Ibhayoloji yeRedox, 65, iphe. 102822. doi: 10.1016/J.REDOX.2023.102822.
