RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (Promoter)
收藏官方服务：
资源简介：
RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (Promoter)
应用场景：
创建时间：
2015-03-31
相关数据集
Identification of Transcription Factor PQM-1::GFP Binding Regions in L3
Identification of Transcription Factor PQM-1::GFP Binding Regions in L3
ChEBI2011-02-18 更新00
TF ChIP-seq from HepG2 (ENCSR764ZBK)
ChIP-Seq on HepG2 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf https://www.encodeproject.org/ENCSR764ZBK/
NIAID Data Ecosystem30
Global consensus map and dynamics of human transcription factor footprints
Data associated with publication "Global reference mapping and dynamics of human transcription factor footprints". https://doi.org/10.1101/2020.01.31.927798 These data describe digital genomic footprints derived from 243 human biosamples. Please see http://vierstra.org/resources/dgf for additional information and a complete set of raw DNase I data. Metadata with biosample annotation and ENCODE project accessions in Excel format (Extended Data Table 1): Consensus_footprints_metadata.xlsx Motif clustering metdata in Excel format (Extended Data Table 2): Motif_clustering_metadata.xlsx Raw footprint call within individual datasets at a FDR cutoff of 0.01 (additional levels of FDR thresholding can be made available by request). The following tarball contains 243 BED-formatted files, each corresponding to an individual dataset. (Extended Data File 1). Footprints_per_sample.0q01.tar.gz Tab-delimited files with consensus footprint coordinates and overlaps with matches to motif model clusters in human genome build GRCh38/hg38. The legend file contains column definitions in detail (Extended Data File 2). Consensus_footprints_and_motifs_hg38.bed.gz Consensus_footprints_and_motifs_legend.txt BED-formatted file containing the coordinates for clustered motif model matches that overlap consensus footprints (Extended Data File 3) Collapsed_motifs_overlaping_consensus_footprints.bed.gz Collapsed_motifs_overlaping_consensus_footprints_legend.txt Footprint occupancy matrix of index footprints (rows) vs. biosamples (columns). Rows are same order as the consensus footprint file and columns are same order as in the metadata files (Extended Data Files 4 and 5). Consensus_footprints_and_motifs_matrix_full_hg38.txt.gz (Values are -log(1-posterior)) Consensus_footprints_and_motifs_matrix_binary_hg38.txt.gz (binary occupancy matrix, where footprints with posterior footprint probability >0.99 are considered occupied) Single nucleotide variants tested for allelic imbalance. The legend file contains column definitions in detail (Extended Data File 6). De_novo_SNVs_tested_for_imbalance.bed.gz De_novo_SNVs_tested_for_imbalance.legend.txt Contact: Jeff Vierstra (jvierstra@altius.org)
Zenodo2020-08-01 更新00
DNA recognition sequence of PAS heterodimers.
1 The names of the recognition sites are indicated: CNS midline enhancer (CME), hypoxia response element (HRE), xenobiotic response element (XRE) and the E box is the recognition site for bHLH proteins. Similar (Sima) is the fly hypoxia inducible factor-α, Spineless (Ss) functions in bristle, leg and antennal development and Period (Per), Timeless (Tim), Clock and Bmal function in circadian rhythms. 2 The CGTG core sequences shared by each recognition site are italicized. 3 The GCGTG and ACGTG sites are likely low affinity sites for Dys/Tgo [58].
NIAID Data Ecosystem50
A fully validated blood stem/progenitor cell regulatory network reveals mechanisms of cell state stabilisation
The aim of this study was to determine the genomic binding sites of important haematopoietic transcription factors in haematopoietic cell lines. 416Bs cells were fixed with either 1 or 0.4 % formaldehyde for 10 mins. Chromatin was isolated, sonicated for 7 mins (30 sec on, 30 sec off), and specific antibodies were used to pull down the transcription factors of interest after a pre-clearing step. Chromatin was washed, de-crosslinked, amplified, size selected by gel purification and sequenced.
NIAID Data Ecosystem30
Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes
Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes
ChEBI2011-10-06 更新10
Additional file 2 of Evaluating tools for transcription factor binding site prediction
Evaluation of search tools using JASPAR.2010 PWMs. Sensitivity, Positive predictive value, Geometric accuracy and False positive rate for the 14 TFBSs that are found in the PAZAR-J dataset. Separate sheets are provided for each of the search tools. (XLS 31.5 kb)
DataCite Commons2020-07-14 更新60
TF ChIP-seq from heart left ventricle (ENCSR718SDR)
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf https://www.encodeproject.org/ENCSR718SDR/
NIAID Data Ecosystem70
Genome-wide maps of SMXL6 binding sites in Arabidopsis seedlings [pSMXL6:SMXL6-HA]
Purpose: SMXL6 is a key repressor in strigolactone signaling. The goal of this study is to identify the targeted genes of SMXL6 in the model plant Arabidopsis thaliana. Methods: The stable pSMXL6:SMXL6-HA transgenic line in the smxl6/7/8 background and the smxl6/7/8 mutant were grown for two weeks in 0.5 x MS medium and collected for extraction of the protein-DNA complexes. After ChIP analyses, DNA profiles were generated by deep sequencing, in double replicate, using Illumina system Novaseq 6000. The sequence reads were analyzed using BWA software and SAMtools. ChIP-qPCR validation was performed using Bio-Rad CFX 96 real-time PCR detection system. Results: We identified 1665 and 1401 peaks in replicate experiment 1 and 2. Investigating the binding sites of SMXL6 in the smxl6/7/8 pSMXL6:SMXL6-HA transgenic plants, using the smxl6/7/8 mutant as a control.
NIAID Data Ecosystem30
CUT&RUN profiling of genomic BFD1 binding sites. CUT&RUN profiling of genomic BFD1 binding sites
Using an epitope-tagged BFD1-complemented strain, the genomic binding of BFD1 was assessed in alkaline-stress induced bradyzoites. Overall design: One experimental (anti-Ty) and one control (Isotype) sample
NIAID Data Ecosystem20
Tiling Array HSF immunopurification. Drosophila melanogaster
Mapping of in vivo Heat Shock Factor binding sites in drosophila embryos with genomic tiling arrays Keywords: repeat sample
NIAID Data Ecosystem50
BCL11B DNA binding sites in progenitor and differentiated populations in the human thymus. Homo sapiens
To define binding targets during thymopoiesis on a genome wide scale, we performed ChIP-Seq for BCL11B on two cell types isolated from the human thymus: the CD34+ progenitors and the more differentiated CD34- cells Overall design: ChIP-Seq for BCL11B binding was done on CD34+ and CD34- cells isolated from human thymus (n=2 biological replicates per cell type)
NIAID Data Ecosystem20
The cistrome of NKX3.1 in LNCaP prostate cancer cells
Here we report the genome-wide set of factors bound by NKX3.1 or control IgG in human prostate cancer cells (LNCaP). Overall design: Examination of NKX3.1 binding in LNCaP prostate cancer cells
NIAID Data Ecosystem50
TF ChIP-seq from K562 (ENCSR124YFA)
ChIP-Seq on K562 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf https://www.encodeproject.org/ENCSR124YFA/
NIAID Data Ecosystem00
Genome-wide binding of FOXD3 in mouse ESCs
We performed streptavidin pulldown sequencing of endogenously and exogenously Avi-tagged FOXD3 to determine genome-wide binding pattern of this transcription factor in asynchronous or cell cycle synchronized naive mouse ESCs. Overall design: Endogenously Avi-tagged FOXD3 was compared to non-BirA expressing cells and exogeneously Avi-tagged FOXD3 was compared to non-induced cells.
NIAID Data Ecosystem10
Summary of common TFBs found in the upstream of NANOGP8 isolated from the gDNA and exosomal DNA clones.
Summary of common TFBs found in the upstream of NANOGP8 isolated from the gDNA and exosomal DNA clones.
Figshare2023-01-25 更新20
Direct CtrA regulon.
The direct CtrA regulon is composed of genes that are differentially expressed upon CckA and/or ChpT depletion (S1 Data) and have a CtrA binding site as observed by ChIP-seq (S6 Data) or of genes that are in an operon with such genes. Genes that are present in the same operon (predicted by DOOR2) are highlighted in the same color. The functional classification of these genes was performed by manual annotation using the Uniprot database and is also reflected by the COG categories. (XLSX)
NIAID Data Ecosystem10
TF ChIP-seq from A549 (ENCSR161CZA)
eGFP-ATOH8 ChIP-seq on human A549 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf https://www.encodeproject.org/ENCSR161CZA/
NIAID Data Ecosystem30
De-Novo Identification of PPARγ/RXR Binding Sites and Direct Targets during Adipogenesis
BackgroundThe pathophysiology of obesity and type 2 diabetes mellitus is associated with abnormalities in endocrine signaling in adipose tissue and one of the key signaling affectors operative in these disorders is the nuclear hormone transcription factor peroxisome proliferator-activated receptor-γ (PPARγ). PPARγ has pleiotropic functions affecting a wide range of fundamental biological processes including the regulation of genes that modulate insulin sensitivity, adipocyte differentiation, inflammation and atherosclerosis. To date, only a limited number of direct targets for PPARγ have been identified through research using the well established pre-adipogenic cell line, 3T3-L1. In order to obtain a genome-wide view of PPARγ binding sites, we applied the pair end-tagging technology (ChIP-PET) to map PPARγ binding sites in 3T3-L1 preadipocyte cells. Methodology/Principal FindingsCoupling gene expression profile analysis with ChIP-PET, we identified in a genome-wide manner over 7700 DNA binding sites of the transcription factor PPARγ and its heterodimeric partner RXR during the course of adipocyte differentiation. Our validation studies prove that the identified sites are bona fide binding sites for both PPARγ and RXR and that they are functionally capable of driving PPARγ specific transcription. Our results strongly indicate that PPARγ is the predominant heterodimerization partner for RXR during late stages of adipocyte differentiation. Additionally, we find that PPARγ/RXR association is enriched within the proximity of the 5′ region of the transcription start site and this association is significantly associated with transcriptional up-regulation of genes involved in fatty acid and lipid metabolism confirming the role of PPARγ as the master transcriptional regulator of adipogenesis. Evolutionary conservation analysis of these binding sites is greater when adjacent to up-regulated genes than down-regulated genes, suggesting the primordial function of PPARγ/RXR is in the induction of genes. Our functional validations resulted in identifying novel PPARγ direct targets that have not been previously reported to promote adipogenic differentiation. Conclusions/SignificanceWe have identified in a genome-wide manner the binding sites of PPARγ and RXR during the course of adipogenic differentiation in 3T3L1 cells, and provide an important resource for the study of PPARγ function in the context of adipocyte differentiation.
NIAID Data Ecosystem50
PolII transcription factor in Human HeLa S3
We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor PolII in HeLa S3 cells. The PolII ChIP was performed according to the same protocol as used for the STAT1 samples except that the cells were not stimulated using gamma-interferon prior to formaldehyde fixation. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of the PolII transcription factor in Human HeLa S3.
NIAID Data Ecosystem20
