[PDF] Top 20 Identification of transcription factor binding sites using ATAC seq
Has 10000 "Identification of transcription factor binding sites using ATAC seq" found on our website. Below are the top 20 most common "Identification of transcription factor binding sites using ATAC seq".
Identification of transcription factor binding sites using ATAC seq
... respectively. ATAC- seq libraries were sequenced with a Illumina NextSeq 500 Platform with 75 bps paired-end reads in ...other ATAC-seq ... See full document
21
PhyloScan: identification of transcription factor binding sites using cross-species evidence
... algorithms using real sequence data is difficult, because of the presence of tran- scription factor binding sites that are likely real, but unre- ...predicted sites reported as false ... See full document
17
An information transmission model for transcription factor binding at regulatory DNA sites
... The transcription of genes is controlled by transcription factors (TFs), which bind to short DNA motifs that are known as transcription factor binding sites ...(TFBSs). ... See full document
15
Identification of an Adeno-Associated Virus Rep Protein Binding Site in the Adenovirus E2a Promoter
... Rep68 binding to the E2a promoter region by ...the binding of purified Rep68 to the 303-bp fragment by ...the binding site in the AAV ...nucleotide binding site) bound to the 303-bp fragment ... See full document
11
Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
... on ATAC-seq. Figure S1. Differential binding analysis identifies depot-specific chromatin accessibil- ity in ...by ATAC-seq from different subjects (Sub1 and Sub2), fat depots ... See full document
15
Mapping genome-wide transcription factor binding sites in frozen tissues
... genome-wide binding profiles using chromatin from as lit- tle as ≈675,000 ...of binding sites that were shared even between 5 mg biological replicates (Additional file 1: Table ...of ... See full document
10
Identification of dynamic glucocorticoid-induced methylation changes at the FKBP5 locus
... of transcription factor binding derived from chromatin immunoprecipitation (ChIP) experiments in multiple cell lines from the ENCODE project; CTCF-ChIA-PET and PolII- ChIA-PET — track indicating the ... See full document
14
Temozolomide analog PMX 465 downregulates MGMT expression in HCT116 colorectal carcinoma cells
... Sp1 binding sites, and transcription factor Sp1 binding could promote MGMT expression(Bocangel et ...Sp1 binding to its consensus site in the MGMT promoter, we performed EMSA ... See full document
19
Identification and expression profiling of Pht1 phosphate transporters in wheat in controlled environments and in the field
... MYB transcription factor PHR1 activates several Pi starvation-induced genes by binding to the P1BS promoter element (Rubio et ...finger transcription factor have been reported to be ... See full document
16
Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites
... usage using an RNA-Seq plant-pathogen study, however pro- moter sequences from any organism can be analyzed using Marina as long as compatible TFBS models are ... See full document
11
A survey of motif discovery methods in an integrated framework
... ing sites and sequence elements affecting the 3-dimen- sional fold of the chromatin ...the binding sites for transcription factors that will be discussed ... See full document
16
Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions
... the binding site are independent, and the contribution at one position of the binding site to the overall affinity does not de- pend on the identity of nucleotides in other positions of the ...TF ... See full document
14
DNA Replication Efficiency Depends on Transcription Factor-Binding Sites
... T-ag binding at site I posited in the model ...Sp1 sites would also remove weak T-ag binding at site ...of transcription factor-binding sites is required to induce ... See full document
8
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
... and transcription factor binding is not straight- forward, accessible chromatin generally facilitates association of transcription factors to ...their binding site, which may recruit ... See full document
18
Genomic effects of the vitamin D receptor: Potentially the link between vitamin D, immune cells, and multiple sclerosis
... 1; ATAC-seq, assay for transposase-acces- sible chromatin using sequencing; C/EBP, CCAAT/enhancer-binding protein; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; ChIP- ... See full document
14
Genome Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae
... transforming CEN.PK 113-5D with a Kluyveromyces lactis URA3 (KlURA3) marker gene (from vector pWJ1042 [31]) flanked by 45-bp upstream and downstream sequences of the CST6 coding region and screening on synthetic complete ... See full document
10
The demarcation of transcription factor binding sites through the analysis of DNase seq data
... Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell ... See full document
174
High resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP seq
... DNase I digestion was started with the addition of 0.5, 0.3, 0.2, and 0.1 units (U) of DNase I (corre- sponding to a final concentration of 1, 0.6, 0.4, and 0.2 U/ml) (Takara) and incubated at 378C with shaking (230 rpm) ... See full document
14
Reproducible inference of transcription factor footprints in ATAC seq and DNase seq datasets using protocol specific bias modeling
... but using a uni- form background, which is equivalent to no bias correction (see The “Methods” ...and ATAC-seq (Additional file 1: Figure S5B; IDR thresholds agreed well with observed ...in ... See full document
13
Molecular characterisation of murine Nfe2l1
... by using PCR primers designed either to connect two exons or to be intronic: pseudogenes are most commonly ...analysis using a UTR-specific probe may also determine if the PACs contain a closely related ... See full document
247
Related subjects