RegulonDB RegulonDB 9.4: High-throughput Datasets

High-throughput Datasets


The datasets classified in this page are high-throughput data manually curated. In some cases not all data from the paper are reported in the files, only those that have the properties described in the Description Document.

   
Genomic SELEX   
Dataset summary Datasets Author Evidence DownLoad Files
CRP dataset. Genomic SELEX screening and computational analysis were performed to identify the whole set of CRP regulation targets. A total of 265 new regulatory interactions were identified by the two methods.
See details of the dataset in the description document.
 
265 Regulatory Interactions by gSELEX and IHBCE Shimada T. et al. Weak evidence
(gSELEX,IHBCE)
Datafile
H-NS dataset. Genomic SELEX screening and microarray analysis were performed to identify the whole set of LeuO and H-NS regulation targets. A total of 987 H-NS-binding peaks (1,060 regulatory interactions) were identified via the SELEX methodology, and 77 regulatory interactions were found by combining data from both the SELEX and microarray analyses.
See details of the dataset in the description document.
 
1060 Regulatory Interactions by gSELEX Shimada T. et al. Strong evidence
(gSELEX)
Datafile
77 Regulatory Interactions by gSELEX,GEA Shimada T. et al. Strong evidence
(gSELEX, GEA, CV(gSELEX/GEA))
Datafile
LeuO dataset. Genomic SELEX screening and microarray analysis were performed to identify the whole set of LeuO and H-NS regulation targets. A total of 140 LeuO-binding peaks (183 regulatory interactions) were identified by using the SELEX methodology, and 35 regulatory interactions were found by combining data from both the SELEX and microarray analyses.
See details of the dataset in the description document.
 
183 Regulatory Interactions by gSELEX Shimada T. et al. Strong evidence
(gSELEX)
Datafile
35 Regulatory Interactions by gSELEX and GEA Shimada T. et al. Strong evidence
(gSELEX,GEA, CV(gSELEX/GEA))
Datafile


ChIP-exo   
Dataset summary Datasets Author Evidence DownLoad Files
GadEWX dataset from ChIP-exo experiments. GadEWX regulons consist of 45 target genes in 31 TUs and 28 of these genes were associated with RpoS-binding sites. ChIP-exo was also used to determine the in vivo binding profile of RpoS under acid stress.
See details of the dataset in the description document.
Peaks: GadE (16), GadW (6), GadX (41). Seo SW et al. ChIP analysis and statistical validation of TFBSs (CHIP-SV) and Mapping of signal intensities by RNA-seq (MSI). Datafile

OxyR and SoxRS dataset from ChIP-exo and RNA-seq analysis .OxyR and SoxRS regulons were determined under oxidative stress (paraquat treatment) based on ChIp-exo and RNA-seq analysis. These consist of 68 genes in 51 transcription units. Among them, 48 genes in 36 TUs showed more than 2-fold changes in expression level under single-TF- knockout conditions. Their roles include direct activation of amino acid biosynthesis, cell wall synthesis, and divalent metal ion transport.
See details of the dataset in the description document.
Peaks: OxyR (29), SoxR (10), SoxS (26). Seo SW et al. ChIP analysis and statistical validation of TFBSs (CHIP-SV) and Mapping of signal intensities by RNA-seq (MSI). Datafile


RNA-seq   
Dataset summary Datasets Author Evidence DownLoad Files
High-throughput transcription initiation mapping. Illumina directional RNA-seq experiments were total RNA received different treatments to enrich for 5' monophosphate or 5' triphosphate ends. Version 3.0.
See details of the dataset in the description document.
  Morett E. et al. Strong evidence Datafile

High-throughput transcription initiation mapping
See details of the dataset in the description document.
  Morett E. et al. Weak evidence Datafile

5'-RACE transcription initiation mapping with specific primers.
See details of the dataset in the description document.
  Morett E. et al. Strong evidence Datafile

Transcriptional start sites (TSS) in the E. coli K12 MG1655 genome detected by combining a differential RNA-seq (dRNA-seq) approach.
See details of the dataset in the description document.
LB_0.4, grown to exponential (OD600 ~0.4) in LB medium. Storz G, et al. Strong evidence
(RS-EPT-CBR)
Datafile
LB_2.0, grown to stationary phase (OD600 ~2.0) in LB medium Storz G, et al. Strong evidence
(RS-EPT-CBR)
Datafile
M63_0.4, grown to exponential phase (OD600 ~0.4) in M63 minimal glucose medium. Storz G, et al. Strong evidence
(RS-EPT-CBR)
Datafile


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