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Hi-C raws Chromatin Interaction
Hi-C yog ib txoj hauv kev tsim los ntes genomic configuration los ntawm kev sib txuas kev soj ntsuam kev sib thooj-raws li kev sib raug zoo thiab kev sib tw siab. Cov txheej txheem yog ua raws li chromatin crosslinking nrog formaldehyde, ua raws li kev zom zaub mov thiab rov ua dua tshiab nyob rau hauv ib txoj kev uas tsuas yog cov seem uas txuas nrog covalently yuav tsim cov khoom ligation. Los ntawm kev ua raws cov khoom lag luam ligation, nws tuaj yeem kawm txog 3D lub koom haum ntawm genome. Hi-C tso cai rau kev kawm txog kev faib tawm ntawm feem ntawm cov genome uas tau ntim me me (A compartments, euchromatin) thiab feem ntau yuav ua rau muaj kev cuam tshuam, thiab cov cheeb tsam uas ntim ntau dua (B compartments, Heterochromatin). Hi-C kuj tuaj yeem siv los txheeb xyuas Topologically Associated Domains (TADs), thaj chaw ntawm cov genome uas muaj cov qauv sib dhos thiab yuav muaj cov qauv qhia zoo sib xws, thiab txhawm rau txheeb xyuas cov chromatin loops, thaj tsam DNA uas tau koom ua ke los ntawm cov proteins thiab uas yog feem ntau enriched nyob rau hauv kev cai hais. BMKGene's Hi-C sequencing service pab txhawb cov kws tshawb fawb los tshawb txog qhov loj me ntawm genomics, qhib txoj hauv kev tshiab rau kev nkag siab txog kev tswj hwm genome thiab nws qhov cuam tshuam rau kev noj qab haus huv thiab kab mob.
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Chromatin Immunoprecipitation Sequencing (ChIP-seq)
Chromatin Immunoprecipitation (CHIP) yog ib qho txheej txheem uas siv cov tshuaj tiv thaiv kab mob los xaiv kom txhawb nqa DNA-binding proteins thiab lawv cov hom phiaj genomics sib xws. Nws kev koom ua ke nrog NGS ua rau lub genome-wide profileing ntawm DNA lub hom phiaj cuam tshuam nrog kev hloov kho histone, cov ntaub ntawv hloov pauv, thiab lwm yam DNA-binding proteins. Txoj hauv kev zoo li no ua rau muaj kev sib piv ntawm cov chaw sib txuas ntawm ntau hom ntawm tes, cov ntaub so ntswg, lossis cov xwm txheej. Chip-Seq cov ntawv thov nthuav tawm los ntawm kev kawm txog kev tswj hwm kev hloov pauv thiab txoj hauv kev loj hlob mus rau elucidating kab mob mechanisms, ua rau nws yog ib qho cuab yeej tseem ceeb rau kev nkag siab txog genomic regulation toj roob hauv pes thiab ua kom pom kev kho mob.
Platform: Illumina NovaSeq
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Tag nrho genome bisulfite sequencing (WGBS)
Tag Nrho Genome Bisulfite Sequencing (WGBS) yog tus qauv kub-txheej txheem rau kev tshawb nrhiav qhov tob ntawm DNA methylation, tshwj xeeb yog txoj haujlwm thib tsib hauv cytosine (5-mC), qhov tseem ceeb ntawm kev tswj cov noob qhia thiab kev ua haujlwm ntawm tes. Lub hauv paus ntsiab lus ntawm WGBS suav nrog kev kho bisulfite, ua rau kev hloov pauv ntawm unmethylated cytosines rau uracil (C rau U), thaum tawm hauv methylated cytosine tsis hloov. Cov txheej txheem no muaj kev daws teeb meem ib leeg, tso cai rau cov kws tshawb fawb los tshawb xyuas cov methylome thiab nthuav tawm cov qauv methylation txawv txav cuam tshuam nrog ntau yam mob, tshwj xeeb yog mob qog noj ntshav. Los ntawm kev ua haujlwm WGBS, cov kws tshawb fawb tuaj yeem tau txais kev nkag siab tsis sib xws rau hauv genome-wide methylation toj roob hauv pes, muab kev nkag siab zoo ntawm cov txheej txheem epigenetic uas ua rau muaj ntau yam kab mob lom neeg thiab kab mob.
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Kev ntsuam xyuas rau Transposase-Accessible Chromatin nrog High Throughput Sequencing (ATAC-seq)
ATAC-seq yog cov txheej txheem kev sib tw ua haujlwm siab uas siv rau genome-wide chromatin accessibility tsom xam. Nws siv muab kev nkag siab tob txog cov txheej txheem nyuaj ntawm kev tswj hwm lub ntiaj teb epigenetic ntawm cov noob qhia. Cov txheej txheem siv lub hyperactive Tn5 transposase rau ib txhij fragment thiab tag qhib chromatin cheeb tsam los ntawm inserting sequencing adaptors. Tom qab PCR amplification tshwm sim nyob rau hauv lub creation ntawm ib tug sequencing tsev qiv ntawv, uas tso cai rau kom paub meej qhia txog qhib chromatin cheeb tsam nyob rau hauv tej chaw-lub sij hawm tej yam kev mob. ATAC-seq muab kev pom zoo ntawm cov chaw chromatin siv tau, tsis zoo li cov txheej txheem uas tsuas yog tsom mus rau qhov chaw sib txuas lus los yog cov cheeb tsam tshwj xeeb-hloov kho. Los ntawm kev ua raws cov cheeb tsam qhib chromatin, ATAC-seq qhia cov cheeb tsam uas yuav muaj feem cuam tshuam rau cov kev cai tswj hwm thiab muaj peev xwm hloov pauv qhov cuam tshuam qhov chaw, muab kev nkag siab zoo rau hauv kev hloov pauv ntawm cov noob qhia thoob plaws genome.
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Txo Cov Neeg Sawv Cev Bisulfite Sequencing (RRBS)
Txo Cov Neeg Sawv Cev Bisulfite Sequencing (RRBS) tau tshwm sim los ua tus nqi tsim nyog thiab muaj txiaj ntsig zoo rau Whole Genome Bisulfite Sequencing (WGBS) hauv DNA methylation kev tshawb fawb. Thaum WGBS muab kev nkag siab zoo los ntawm kev tshuaj xyuas tag nrho cov genome ntawm ib qho kev daws teeb meem, nws tus nqi siab tuaj yeem yog qhov txwv. RRBS tau tawm tswv yim txo qhov kev sib tw no los ntawm kev xaiv kev tshuaj xyuas ib feem ntawm cov genome. Cov txheej txheem no tso siab rau kev txhawb nqa ntawm CpG cov kob-nplua nuj cheeb tsam los ntawm MspI cleavage ua raws li kev xaiv loj ntawm 200-500/600 bps fragments. Yog li ntawd, tsuas yog thaj tsam ze rau CpG Islands tuaj, thaum cov Islands tuaj CpG nyob deb tsis suav nrog kev tshuaj xyuas. Cov txheej txheem no, ua ke nrog bisulfite sequencing, tso cai rau cov kev daws teeb meem siab ntawm DNA methylation, thiab kev sib txuas ua ke, PE150, tsom tshwj xeeb rau qhov kawg ntawm cov ntawv ntxig es tsis yog nruab nrab, ua kom cov txiaj ntsig ntawm methylation profileing. RRBS yog ib qho cuab yeej tseem ceeb uas ua rau muaj txiaj ntsig zoo DNA methylation tshawb fawb thiab txhawb kev paub txog cov txheej txheem epigenetic.
