chromatin immunoprecipitation sequencing...2020/01/18 · jnk_dn.v1_up wnt_up.v1_dn rb_dn.v1_dn...
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ChIP-Seq provides genome-wide profiling of DNA targets for histone modifica-tion, transcription factors, and other DNA-associated proteins. It combines the selectivity of chromatin immuno-precipitation (ChIP) to recover specific protein-DNA complexes, with the power of next-generation sequencing (NGS) for high-throughput sequencing of the recovered DNA. Additionally, because the protein-DNA complexes are recovered from living cells, binding sites can be compared in different cell types and tissues, or under different conditions. Applications range from transcriptional regulation to developmental pathways to disease mechanisms and beyond.
At Novogene, we provide high-quality sequencing and comprehensive bioinfor-matics solutions for your ChIP-Seq projects.
Project Workflow
SamplePreparation
LibraryConstruction Sequencing Bioinformatics
Analysis
Sample QualityControl
Library QualityControl
Data QualityControl
Specifications
SAMPLE REQUIREMENTS• DNA quantity: ≥ 50 ng, main peak locates between 100 to 500 bp• Sample volume: ≥ 10 μl• OD260/280 = 1.8 to 2.0 without degradation or RNA contamination
SEQUENCING STRATEGY• 100-500 bp insert DNA library (depending on peak distribution)• NovaSeq platform, paired-end 150 bp
TURNAROUND TIME• 22 business days for 20 or fewer samples, from the time sample quality is verified*
RECOMMENDED DATA OUTPUT• ≥6 Gb per sample
Novogene Advantages
Cost-Effective and Quick Turnaround:Rapid and efficient genome-wide profiling of multiple samples at very competitive prices.
Comprehensive Analysis: Using the widely accepted MACS2 software and the latest programs for peak annotation, motif prediction, functional analysis and data visualization, we offer analysis solutions to meet your project needs.
Data and Analysis Guarantee:Our team of experienced scientists ensure the data and analysis quality to be publication ready.
Extensive Experience: Over 2000 projects successfully completed.
Chromatin Immunoprecipitation Sequencing
Mutations or aberrant upregulation of EZH2 occur frequently in human cancers. In this study, the results of H3K27ac ChIP-seq, RNA-seq, and proteomics analysis demonstrated that H3K27ac upregulation, due to EZH2 inhibition, results in the transcrip-tional activation of multiple onco-pathways in a cell-context-dependent manner. This may also underline the resistance to EZH2i.
Analysis Pipeline
Targeting Epigenetic Crosstalk as a Therapeutic Strategy for EZH2-Aberrant Solid Tumors (Huang 2018)
* For projects without data analysis.For Research Use Only. Exclusive for Clients in North and South America.
Figure 1. Feedback H3K27 Acetylation Change Drives Oncogenic Transcriptional Reprogramming.
Novogene Client Publication
H3K27ac
70
70EPZ
DMSO
2kb
CTNNB1
0
0
H3K27ac ChIP-seq
PTEN_DN.V2_UP
Enr
ichm
ent s
core NES=1.56
Q=0.02P=0.002
U2932
ControlEPZ
VEGF_A_UP.V1_UP
Enr
ichm
ent s
core
NES=1.60Q=0.002P=0
U2932
ControlEPZ
RNA-seq
KRAS.50_UP.V1_UP
Enr
ichm
ent s
core NES=1.78
Q=0.002P=0
SMMC-7721
ControlEPZ
MYC_UP.V1_UP
Enr
ichm
ent s
core
NES=1.69Q=0.0005P=0
U2932
ControlEPZ
Proteome
MEK_UP.V1_UP
Enr
ichm
ent s
core
NES=2.43Q=0.0008P=0
U2932
ControlEPZ
WNT_UP.V1_UP
Enr
ichm
ent s
core
NES=2.12Q=0.009P=0.001
SMMC-7721
ControlEPZ
RNA-seq
0 0.02 0.06 0.1FDR
ProteomeH3K27ac ChIP-seq
AKT_UP.V1_DNMTOR_UP.V1_UPATF2_UP.V1_DNSTK33_NOMO_DNSTK33_SKM_DNSTK33_DNE2F3_UP.V1_UPPIGF_UP.V1_UPYAP1_UPVEGF_A_UP.V1_DNRB_P130_DN.V1_DNTBK1.DF_DNKRAS.50_UP.V1_UPBCAT_BILD_ET_AL_UPNRL_DN.V1_DNTBK1.DF_UPP53_DN.V2_DNCRX_NRL_DN.V1_DNNFE2L2.V2PDGF_ERK_DN.V1_UPCAHOY_ASTROCYTICIL2_UP.V1_UPPTEN_DN.V2_DNESC_V6.5_UP_EARLY.V1_UPATF2_UP.V1_UPCYCLIN_D1_KE_.V1_UPAKT_UP_MTOR_DN.V1_DNRELA_DN.V1_UPCORDENONSI_YAP_CONSERVED_SIGNATURERB_P107_DN.V1_UPATM_DN.V1_DNGCNP_SHH_UP_EARLY.V1_DNGCNP_SHH_UP_LATE.V1_DNCTIP_DN.V1_UPSRC_UP.V1_UPNRL_DN.V1_UPALK_DN.V1_UPPDGF_UP.V1_DNRPS14_DN.V1_DNRB_DN.V1_UPEIF4E_UPHINATA_NFKB_IMMU_INFSIRNA_EIF4GI_UPSNF5_DN.V1_UPPRC2_SUZ12_UP.V1_UPATF2_S_UP.V1_UPSINGH_KRAS_DEPENDENCY_SIGNATURE_HOXA9_DN.V1_DNCAMP_UP.V1_UPMTOR_UP.N4.V1_UPCYCLIN_D1_UP.V1_UPESC_V6.5_UP_LATE.V1_DNCRX_DN.V1_UPRB_P130_DN.V1_UPMYC_UP.V1_UPKRAS.50_UP.V1_DNIL15_UP.V1_UPPRC2_EED_UP.V1_DNESC_J1_UP_LATE.V1_DNESC_J1_UP_EARLY.V1_DNPDGF_ERK_DN.V1_DNHOXA9_DN.V1_UPMTOR_UP.N4.V1_DNEGFR_UP.V1_DNMEK_UP.V1_DNSTK33_SKM_UPSTK33_UPBCAT.100_UP.V1_DNSTK33_NOMO_UPRPS14_DN.V1_UPKRAS.600_UP.V1_UPKRAS.300_UP.V1_UPPTEN_DN.V1_UPCAHOY_ASTROGLIALIL15_UP.V1_DNCSR_LATE_UP.V1_DNP53_DN.V1_DNESC_J1_UP_LATE.V1_UPESC_V6.5_UP_LATE.V1_UPMEK_UP.V1_UPKRAS.KIDNEY_UP.V1_UPRAF_UP.V1_DNATF2_S_UP.V1_DNCRX_DN.V1_DNMEL18_DN.V1_DNBMI1_DN_MEL18_DN.V1_DNBMI1_DN.V1_DNBCAT_GDS748_UPLEF1_UP.V1_DNIL2_UP.V1_DNKRAS.LUNG.BREAST_UP.V1_DNKRAS.LUNG_UP.V1_DNKRAS.600_UP.V1_DNKRAS.600.LUNG.BREAST_UP.V1_DNKRAS.300_UP.V1_DNRAF_UP.V1_UPKRAS.DF.V1_UPERB2_UP.V1_UPLTE2_UP.V1_UPEGFR_UP.V1_UPPTEN_DN.V1_DNCYCLIN_D1_UP.V1_DNAKT_UP_MTOR_DN.V1_UPCYCLIN_D1_KE_.V1_DNKRAS.PROSTATE_UP.V1_DNKRAS.LUNG_UP.V1_UPPTEN_DN.V2_UPRAPA_EARLY_UP.V1_UPKRAS.LUNG.BREAST_UP.V1_UPPRC2_EED_UP.V1_UPPRC2_EZH2_UP.V1_DNBRCA1_DN.V1_DNCAHOY_OLIGODENDROCUTICKRAS.600.LUNG.BREAST_UP.V1_UPPIGF_UP.V1_DNKRAS.KIDNEY_UP.V1_DNPKCA_DN.V1_UPRELA_DN.V1_DNBMI1_DN_MEL18_DN.V1_UPMEL18_DN.V1_UPWNT_UP.V1_UPIL21_UP.V1_DNJNK_DN.V1_DNTGFB_UP.V1_DNSNF5_DN.V1_DNLEF1_UP.V1_UPKRAS.PROSTATE_UP.V1_UPESC_V6.5_UP_EARLY.V1_DNBMI1_DN.V1_UPTGFB_UP.V1_UPJAK2_DN.V1_UPMTOR_UP.V1_DNVEGF_A_UP.V1_UPPRC1_BMI_UP.V1_UPKRAS.AMP.LUNG_UP.V1_DNNOTCH_DN.V1_DNATM_DN.V1_UPCRX_NRL_DN.V1_UPNOTCH_DN.V1_UPLTE2_UP.V1_DNP53_DN.V1_UPCTIP_DN.V1_DNE2F1_UP.V1_DNAKT_UP.V1_UPBCAT.100_UP.V1_UPESC_J1_UP_EARLY.V1_UPKRAS.BREAST_UP.V1_DNCAMP_UP.V1_DNCAHOY_NEURONALIL21_UP.V1_UPBRCA1_DN.V1_UPKRAS.BREAST_UP.V1_UPDCA_UP.V1_UPMYC_UP.V1_DNKRAS.DF.V1_DNP53_DN.V2_UPALK_DN.V1_DNE2F3_UP.V1_DNKRAS.AMP.LUNG_UP.V1_UPPRC1_BMI_UP.V1_DNCSR_EARLY_UP.V1_DNRAPA_EARLY_UP.V1_DNPRC2_SUZ12_UP.V1_DNPKCA_DN.V1_DNJNK_DN.V1_UPWNT_UP.V1_DNRB_DN.V1_DN
U2932SMMC-7721Pfeiffer
Reference: Huang X, Yan J, Zhang M, . Targeting Epigenetic Crosstalk as a Therapeutic Strategy for EZH2-Aberrant Solid Tumors[J]. , 2018, 175(1): 186-199.Cell
et al
et al,
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Copyright©2011-2020 Novogene Corporation. All Rights Reserved. Information and specifications are subject to change at any time without notice.
Only applicable for projects with comparable experimental groups.
Raw Data QualityControl
SCCAnalysis
MotifPrediction
Peak Calling PeakAnnotation
PeakAnnotation
ReferenceGenomeMapping
Differential Peak analysis
Functional Analysis of Peak-associated
Genes
Functional Analysis of Peak-associated
Genes
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