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Hi-C ku salaysan isdhexgalka Chromatin

Hi-C waa hab loogu talagalay in lagu qabto qaabeynta genomic iyadoo la isku darayo isdhexgalka ku saleysan dhowaanshaha iyo isku xigxiga sareynta. Habka waxa uu ku salaysan yahay iskutallaabta chromatin ee leh formaldehyde, oo ay ku xigto dheefshiidka iyo dib-u-celinta qaab kaliya jajabyada si wadajir ah ugu xiran ayaa samayn doona alaabooyin ligation ah. Iyadoo la raacayo alaabtan ligation, waxaa suurtagal ah in la barto ururka 3D ee genome. Hi-C waxa ay sahlaysa in la barto qaybinta qaybaha genome-ka kuwaas oo si fudud loo soo buuxiyey (Qaybyada A, euchromatin) oo ay u badan tahay in ay si qoraal ah u firfircoon yihiin, iyo gobollada si adag u xidhxidhan (Qaybaha B, Heterochromatin). Hi-C waxa kale oo loo isticmaali karaa in lagu tilmaamo Domains Topologically Associated (TADs), gobollada genome ee leh qaabab isku laabma oo ay u badan tahay in ay leeyihiin qaabab hadal isku mid ah, iyo in la aqoonsado wareegyada chromatin, gobollada DNA ee ay isku dhejiyeen borotiinno iyo kuwan inta badan lagu hodmay xubno nidaamsan. Adeegga isku xigxiga ee BMKGene ee Hi-C waxa uu awood u siiyaa cilmi-baarayaasha in ay sahamiyaan cabbirrada baaxadda genomics-ka, iyaga oo furaya waddooyin cusub oo lagu fahmo nidaamka genome-ga iyo saamaynta ay ku leedahay caafimaadka iyo cudurrada.

Nala Soo Xidhiidh

Faahfaahinta Adeegga

Bioinformatics

Natiijooyinka bandhigga

Daabacaada sifada

Tilmaamaha Adeegga

● Ku darida Illumina NovaSeq oo leh PE150.

Adeeggu wuxuu u baahan yahay muunado unug, halkii laga soo saari lahaa asiidhyada nucleic-ka ah, si looga gudbo formaldehyde oo loo ilaaliyo isdhexgalka borotiinka DNA.

● Tijaabada Hi-C waxay ku lug leedahay xaddidaadda iyo dhammaadka hagaajinta cidhifyada dhegdhegaysan ee biotin, oo ay ku xigto wareegtaynta darafyada aan fiicneyn iyadoo la ilaalinayo isdhexgalka. DNA-da waxaa lagu soo dejiyaa kuulka streptavidin waxaana lagu nadiifiyaa diyaarinta maktabadda xigta.

Faa'iidooyinka Adeegga

●Naqshadeynta Xakamaynta ugu Fiican: si loo hubiyo waxtarka sare ee Hi-C ee noocyada kala duwan oo leh ilaa 93% lammaane is dhexgalka ansax ah.

●Khibrad Balaadhan iyo Diiwaanada Daabacaadda:BMKGene waxay leedahay waayo-aragnimo balaadhan>2000 Hi-C mashruucyo isku xigxiga oo laga soo qaatay 800 nooc oo kala duwan iyo shatiyo kala duwan. In ka badan 100 kiis oo la daabacay oo leh saameyn urursan oo ka badan 900.

●Kooxda Bioinformatics ee xirfad sare leh:leh shatiyada-guriga iyo xuquuqda daabacaadda software-ka ee tijaabooyinka Hi-C iyo falanqaynta xogta iyo software xog muuqaal is-horumariyay.

●Taageerada Iibka Kadib:Ballanqaadkayaga waxa uu dhaafsiisan yahay dhamaystirka mashruuca oo leh 3 bilood oo adeega iibka kadib. Inta lagu jiro wakhtigan, waxaanu bixinaa dabagalka mashruuca, caawinta cilad-raadinta, iyo fadhiyada Q&A si wax looga qabto wixii su'aalo ah ee la xidhiidha natiijooyinka.

●Tibaaxo Dhamaystiran: waxaan isticmaalnaa xog uruurin badan si aan si shaqeyn leh ugu sharaxno hiddo-wadaha kala duwanaansho la aqoonsaday oo aan sameyno falanqaynta kobcinta u dhigma, anagoo bixinayna fikrado ku saabsan mashruucyo cilmi baaris oo badan.

Tilmaamaha Adeegga

Maktabadda

Istaraatiijiyada Taxanaha

Soo saarista xogta lagu taliyay

Xallinta Calaamadaha Hi-C

Hi-C maktabadda

Illumina PE150

Loop Chromatin: 150x

TAD: 50x

Loop Chromatin: 10Kb

TAD: 40Kb

Shuruudaha Adeegga

Tusaalaha nooca	Qadarka loo baahan yahay
Nudaha xoolaha	≥2g
Dhiig dhan	≥2ml
Fungi	≥1g
Plant- nudaha yaryar	1g/aliquot, 2-4 aliquotes ayaa lagula talinayaa
Unugyada Dhaqanka	≥1x10⁷

Kii hore: TGuide Smart Magnetic Plant RNA Kit

Xiga: DNBSEQ horay loo sameeyay maktabadaha

Waxa ku jira Falanqaynta soo socota:

● Xogta ceeriin QC;

● Khariidadeynta iyo maktabadda Hi-C QC: lammaane is dhexgalka ansax ah iyo jibbaarada qudhunka is-dhexgalka (IDEs);

● Xog-ururinta is-dhexgalka-ballaaran ee genome: falanqaynta cis/trans iyo khariidadda isdhexgalka Hi-C;

● Falanqaynta qaybinta A/B;

● Aqoonsiga TAD-yada iyo wareegyada chromatin;

● Falanqaynta kala duwan ee 3D qaab-dhismeedka chromatin ee ka mid ah muunadaha iyo sharraxaadda shaqada ee u dhiganta ee hiddo-wadaha la xidhiidha.

Cis iyo qaybinta saamiga taranka

Khariidadda kulaylka ee isdhexgalka koromosoomyada ee u dhexeeya shaybaarada

Qaybinta Genome-ballaaran ee qolalka A/B

Qaybinta genome-ballaaran ee wareegyada chromatin

Aragtida TADs

Sahami horumarka cilmi-baarista ee ay fududeeyeen adeegyada isku xigxiga ee BMKGene ee Hi-C iyada oo loo marayo ururinta daabacaado la soo xulay.

Meng, T. iyo al. (2021) 'Falanqaynta isku-dhafan ee isku-dhafan ee isbarbardhigga ah ee multi-omics waxay tilmaamaysaa CA2 inay tahay bartilmaameed cusub oo chordoma',Neuro-Oncology, 23 (10), bogga 1709-1722. doi: 10.1093/NEUONC/NOAB156.

Xu, L. iyo al. (2021) 'Habayl la'aanta 3D iyo dib-u-habaynta genome-ga waxay bixisaa aragtiyo ku saabsan pathogenesis ee NAFLD iyadoo la isku daray Hi-C, Nanopore, iyo RNA isku xigxiga',Acta Pharmaceutica Sinica B, 11 (10), bogga 3150–3164. doi: 10.1016/J.APSB.2021.03.022.