|
| Status |
Public on Jun 30, 2014 |
| Title |
Minimal metabolic pathway structure is consistent with associated macromolecular interactions. |
| Organism |
Escherichia coli K-12 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We sequenced mRNA of three dual perturbation experiments of E. coli K12 MG1655 changing both genetic and environmental conditions. Each dual perturbation experiment consists of four RNA-seq samples (WT, WT+nutrient supplementation, transcription factor KO, transcription factor KO+nutrient supplementation). The three conditions are: 1) adenine supplementation/nac KO, 2) L-tryptophan supplementation/cra KO, 3) anaerobic/mntR KO.
|
| |
|
| Overall design |
Determination of whether a transcription factor plays a regulatory role in a particular environmental shift by examining differential expression of mRNA levels.
|
| |
|
| Contributor(s) |
Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO |
| Citation(s) |
24987116 |
| |
| Submission date |
Jun 26, 2013 |
| Last update date |
Jan 04, 2021 |
| Contact name |
Bernhard O Palsson |
| Organization name |
UC San Diego
|
| Department |
Bioengineering
|
| Lab |
Palsson
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0412 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16227 |
Illumina Genome Analyzer IIx (Escherichia coli K-12) |
|
| Samples (14)
|
| GSM1174823 |
Mid log_wildtype_glc minimal media_aerobic rep1 |
| GSM1174824 |
Mid log_wildtype_glc minimal media_aerobic rep2 |
| GSM1174825 |
Mid log_wildtype_glc minimal media_aerobic rep3 |
| GSM1174826 |
Mid log_wildtype_glc minimal media + adenine_aerobic |
| GSM1174827 |
Mid log_wildtype_glc minimal media + L-tryptophan_aerobic |
| GSM1174828 |
Mid log_wildtype_glc minimal media_anaerobic rep1 |
| GSM1174829 |
Mid log_wildtype_glc minimal media_anaerobic rep2 |
| GSM1174830 |
Mid log_wildtype_glc minimal media_anaerobic rep3 |
| GSM1174831 |
Mid log_nac KO_glc minimal media_aerobic |
| GSM1174832 |
Mid log_nac KO_glc minimal media + adenine_aerobic |
| GSM1174833 |
Mid log_cra KO_glc minimal media_aerobic |
| GSM1174834 |
Mid log_cra KO_glc minimal media + L-tryptophan_aerobic |
| GSM1174835 |
Mid log_mntR KO_glc minimal media_aerobic |
| GSM1174836 |
Mid log_mntR KO_glc minimal media_anaerobic |
|
| Relations |
| BioProject |
PRJNA209705 |
| SRA |
SRP026341 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48324_CRA_v_CRA+trp.csv.gz |
42.9 Kb |
(ftp)(http) |
CSV |
| GSE48324_MNTR_v_MNTR_noO2.csv.gz |
41.5 Kb |
(ftp)(http) |
CSV |
| GSE48324_NAC_v_NAC+ade.csv.gz |
42.4 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT+ade_v_NAC+ade.csv.gz |
42.1 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT+trp_v_CRA+trp.csv.gz |
42.8 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT1_noO2_v_MNTR_noO2.csv.gz |
39.7 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT1_v_CRA.csv.gz |
42.3 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT1_v_MNTR.csv.gz |
42.3 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT1_v_NAC.csv.gz |
42.2 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT1_v_WT+ade.csv.gz |
41.9 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT1_v_WT+trp.csv.gz |
42.2 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT2_noO2_v_MNTR_noO2.csv.gz |
41.3 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT2_v_CRA.csv.gz |
42.9 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT2_v_MNTR.csv.gz |
42.9 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT2_v_NAC.csv.gz |
42.8 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT2_v_WT+ade.csv.gz |
42.6 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT2_v_WT+trp.csv.gz |
42.8 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT3_noO2_v_MNTR_noO2.csv.gz |
40.3 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT3_v_CRA.csv.gz |
42.8 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT3_v_MNTR.csv.gz |
42.7 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT3_v_NAC.csv.gz |
42.7 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT3_v_WT+ade.csv.gz |
42.4 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT3_v_WT+trp.csv.gz |
42.7 Kb |
(ftp)(http) |
CSV |
| GSE48324_WT_all_v_WT_noO2_all.csv.gz |
42.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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