Uvavanyo lweChromatin efikelelekayo kwiTransposase ene-High Throughput Sequencing (ATAC-seq)
Iimpawu zeNkonzo
● Inkonzo ifuna iisampulu zezicubu, endaweni yee-nucleic acids ezikhutshiweyo, ukuze kulondolozwe ukusebenzisana kwe-DNA neproteni.
● Indlela ye-ATAC ibandakanya ukwahlukana kwezicubu, kulandele ukwahlukana kwee-nuclei, unyango kunye nokuhlanjululwa kwe-Tn5, ukwandiswa kwe-PCR, ukukhethwa kobukhulu kunye nokulandelelana.
● Ukulandelelana kwe-Illumina NovaSeq
Iingenelo zeNkonzo
●Uvakalelo oluphezulu:Ubungakanani obuphantsi beeseli zokuqala buyanele ukulungiselela nokulandelelanisa ithala leencwadi.
●Ubuchule Obunolwazi Oluphezulu: ngaxeshanye ityhila iindawo ze-genomic ze-chromatin evulekileyo kunye nezinto ezisebenzayo zokulawula ezifana neendawo zokubopha izinto ezibhaliweyo.
●Ukuphinda-phinda okuhle kovavanyo: iikopi zobugcisa zibonisa ukuphindaphindeka okugqwesileyo.
●Ubuchule Obubanzi: kunye namakhulu eeprojekthi zokulandelelanisa ze-ATAC ezigqityiweyo ngempumelelo, i-BMKGENE izisa amava angaphezulu kweshumi leminyaka, iqela lohlalutyo elinobuchule obuphezulu, umxholo opheleleyo, kunye nenkxaso ebalaseleyo emva kokuthengisa.
●Amathuba okujoyina uHlalutyo lweTranscriptomics: okuvumela uhlalutyo oludibeneyo lwe-ATAC seq kunye nezinye idatha ze-omics ezifana ne-RNA-seq.
● Uhlalutyo olupheleleyo lwe-Bioinformatics: okuvumela kungekuphela nje ukuchongwa kweendawo ezivulekileyo ze-chromatin kunye nokusebenza kwazo okuhambelanayo (abakhuthazi, ii-UT, ii-exons, ii-introns) kodwa kunye nohlalutyo lomahluko phakathi kweendawo ezivulekileyo ze-chromatin phakathi kweesampuli.
Iinkcukacha zeNkonzo
| Ithala leeNcwadi | Icebo Lokulandelelanisa | Imveliso yedatha ecetyiswayo | Ulawulo lwemeko |
| I-ATAC-seq | I-Illumina PE150 | > 20M yokufunda Kuxhomekeke kubungakanani be-genome (Umntu: 50 M ufunda) | Q30≥85% |
Iimfuno zeSampuli
Uhlobo lweesampulu: Izicubu, iiseli eziphilayo okanye ezikhenkcezisiweyo, igazi
● Inombolo yeseli: ≥ 106iiseli
● Ubunzima bezicubu: ≥ 200mg izicubu ezintsha
● Igazi: ≥ 4 mL
Ukuhamba komsebenzi wenkonzo
Uyilo lovavanyo
Ukuhanjiswa kwesampulu
Ukukhupha i-DNA
Ukwakhiwa kweThala leeNcwadi
Ukulandelelana
Uhlalutyo lwedatha
Iinkonzo zasemva kokuthengisa
Kubandakanya uHlahlelo Olulandelayo:
● Ulawulo lomgangatho wedatha eluhlaza;
● Ubizo oluphezulu olusekelwe kwimephu ye-genome yesalathiso;
● Inkcazelo ye-gene kwindawo ekwincopho;
● Uhlalutyo lweMotif: ukuchongwa kweendawo zokubopha izinto ezibhaliweyo (TFBS);
● Uhlalutyo lweNqanaba lokwaHlukana kunye nengcaciso.
1. Imephu yobushushu kwi-ATAC ifunda usasazo kwi-TSS nakwiindawo ezikufutshane (±3 kb)
2. Ukusasazwa kwendawo evulekileyo ye-chromatin kwiindawo ezahlukeneyo ze-genome
3. Umahluko phakathi kwamaqela xa kubizwa inani eliphezulu
Hlola inkqubela phambili yophando eququzelelwe ziinkonzo zokulandelelana ze-BMKGene ze-ATAC ngokusebenzisa ingqokelela yeempapasho ezikhethiweyo.
Fu, A.okqhubekayo.(2023) 'I-Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) ityhila uphuhliso lwesiqhamo, ukwakheka kunye neempawu zemfuza ezivuthwayo',Uphando lwezoLimo, 10(1). doi: 10.1093/HR/UHAC228.
UGong, B.okqhubekayo.(2023) 'Ukusebenza kwe-epigenetic kunye ne-transcriptional 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 ukumelana ne-ferroptosis kumhlaza we-colorectal ngokubangela ukucinezelwa kwe-xCT exhomekeke kwi-c-Fos',Ibhayoloji yeRedox, 65, iphe. 102822. doi: 10.1016/J.REDOX.2023.102822.
