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Series GSE142291 Query DataSets for GSE142291
Status Public on Jun 15, 2021
Title Dynamic landscape of protein occupancy across the Escherichia coli chromosome
Organisms Escherichia coli; Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary In bacteria, adaptive regulation of gene expression occurs through the precise interactions of hundreds of DNA binding proteins across the chromosome. Decades of research has revealed the identity and functions of many of these regulators. However, a systems-level understanding of gene expression requires simultaneous, comprehensive monitoring of these interactions as a function of genetic and environmental perturbations. Here we present a high-resolution in vivo protein occupancy display (IPOD-HR) technology that enables quantitative and comprehensive monitoring of DNA-protein interactions across a bacterial chromosome. The global nature of IPOD-HR permits simultaneous activity profiling of all known sequence specific transcription factors and discovery of novel condition-dependent DNA-binding proteins. We show that global IPOD-HR profiles can be used for de novo discovery of sequence specificity motifs for active transcription factors. IPOD-HR also reveals many large domains of extended protein occupancy that define relatively stable, transcriptionally silent regions with unique sequence and gene functional features. IPOD-HR thus provides a unique form of systems-level access to transcriptional regulatory states that will allow rapid profiling and characterization of both known and novel regulatory logic in bacteria. We provide here IPOD-HR occupancy results across a range of genetic and physiological perturbations, as detailed in the accompanying manuscript.
 
Overall design IPOD, Input, and RNA polymerase ChIP data (2 or more replicates each) for cells from each of seven different conditions
 
Contributor(s) Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S
Citation(s) 34170902
Submission date Dec 18, 2019
Last update date Aug 03, 2021
Contact name Peter Freddolino
E-mail(s) petefred@umich.edu
Organization name University of Michigan
Department Biological Chemistry
Lab Freddolino Lab
Street address 1150 W. Medical Center Dr., MSRB 3 room 3315
City Ann Arbor
State/province MI
ZIP/Postal code 48109-0600
Country USA
 
Platforms (4)
GPL14548 Illumina HiSeq 2000 (Escherichia coli)
GPL15010 Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)
GPL21117 Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)
Samples (52)
GSM4224616 WT M9/rdm/glu, no rifampicin, replicate 1, IPOD
GSM4224617 WT M9/rdm/glu, no rifampicin, replicate 2, IPOD
GSM4224618 WT M9/rdm/glu, no rifampicin, replicate 1, input
Relations
BioProject PRJNA596475
SRA SRP238100

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE142291_DargR_m9_rdm_glu_chip_vs_inp_lograt.gr.gz 5.6 Mb (ftp)(http) GR
GSE142291_DargR_m9_rdm_glu_ipod_vs_inp_lograt.gr.gz 5.5 Mb (ftp)(http) GR
GSE142291_DargR_m9_rdm_glu_rzlog10p_chipsub.gr.gz 5.3 Mb (ftp)(http) GR
GSE142291_DlexA_m9_rdm_glu_chip_vs_inp_lograt.gr.gz 5.6 Mb (ftp)(http) GR
GSE142291_DlexA_m9_rdm_glu_ipod_vs_inp_lograt.gr.gz 5.5 Mb (ftp)(http) GR
GSE142291_DlexA_m9_rdm_glu_rzlog10p_chipsub.gr.gz 5.3 Mb (ftp)(http) GR
GSE142291_DpurR_m9_rdm_glu_chip_vs_inp_lograt.gr.gz 5.6 Mb (ftp)(http) GR
GSE142291_DpurR_m9_rdm_glu_ipod_vs_inp_lograt.gr.gz 5.5 Mb (ftp)(http) GR
GSE142291_DpurR_m9_rdm_glu_rzlog10p_chipsub.gr.gz 5.3 Mb (ftp)(http) GR
GSE142291_norif_m9_rdm_glu_chip_vs_inp_lograt.gr.gz 5.4 Mb (ftp)(http) GR
GSE142291_norif_m9_rdm_glu_ipod_vs_inp_lograt.gr.gz 5.4 Mb (ftp)(http) GR
GSE142291_norif_m9_rdm_glu_rzlog10p_chipsub.gr.gz 5.3 Mb (ftp)(http) GR
GSE142291_wt_m9_min_glu_chip_vs_inp_lograt.gr.gz 5.6 Mb (ftp)(http) GR
GSE142291_wt_m9_min_glu_ipod_vs_inp_lograt.gr.gz 5.5 Mb (ftp)(http) GR
GSE142291_wt_m9_min_glu_rna_abundance.tsv.gz 73.3 Kb (ftp)(http) TSV
GSE142291_wt_m9_min_glu_rzlog10p_chipsub.gr.gz 5.3 Mb (ftp)(http) GR
GSE142291_wt_m9_rdm_glu_chip_vs_inp_lograt.gr.gz 5.6 Mb (ftp)(http) GR
GSE142291_wt_m9_rdm_glu_ipod_vs_inp_lograt.gr.gz 5.5 Mb (ftp)(http) GR
GSE142291_wt_m9_rdm_glu_rna_abundance.tsv.gz 73.2 Kb (ftp)(http) TSV
GSE142291_wt_m9_rdm_glu_rzlog10p_chipsub.gr.gz 5.3 Mb (ftp)(http) GR
GSE142291_wt_m9_rdm_glu_statphase_chip_vs_inp_lograt.gr.gz 5.5 Mb (ftp)(http) GR
GSE142291_wt_m9_rdm_glu_statphase_ipod_vs_inp_lograt.gr.gz 5.4 Mb (ftp)(http) GR
GSE142291_wt_m9_rdm_glu_statphase_rna_abundance.tsv.gz 73.7 Kb (ftp)(http) TSV
GSE142291_wt_m9_rdm_glu_statphase_rzlog10p_chipsub.gr.gz 5.3 Mb (ftp)(http) GR
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Processed data are available on Series record
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