GFP_reporters_fix

Reannotation of E. coli transcriptional reporter library (Zaslaver et al. 2006) based on most recent E. coli K-12 genome annotations

• Identification of promoter region amplicons in the most recent E. coli K-12 genome assembly and annotation based on primers provided in the original study using BLAST
• Identification of problematic amplicons and manual error-checking
• Cross-check with RegulonDB
• Linking of amplicons to promoters and their downstream genes
• Script - GFP_fix.py

Files

• GFP_fix.py - Analysis script
• Transcription_factors/ - Information from RegulonDB
• Genome/ - E. coli K-12 genome files and BLAST prep

GFP transcriptionalreporter library annotations

• Info_Dharmacon.xlsx - Library info from Dharmacon provider
• Info_UAL.xls - Library info from the paper (Zaslaver et al. 2006)
• Joined.csv - Clean info

BLAST

• UAL_primers.blast_input - BLAST input file
• UAL_primers_Ecoli_K12_MG1655_U00096.3.blast_output - BLAST output file

E. coli genome with mappings of various features

• Ecoli_K12_MG1655_U00096.3_amplicons.gb - E. coli K-12 genome sequence with amplicons
• Ecoli_K12_MG1655_U00096.3_amplicons_TFBS.gb - E. coli K-12 genome sequence with amplicons and TF binding sites
• Ecoli_K12_MG1655_U00096.3_amplicons_TFBS_Prom.gb - E. coli K-12 genome sequence with amplicons, TF binding sites (RegulonDB) and promoter regions (RegulonDB)
• Ecoli_K12_MG1655_U00096.3_amplicons_TFBS_Prom_Operon.gb - E. coli K-12 genome sequence with amplicons, TF binding sites (RegulonDB), promoter regions (RegulonDB) and operons (RegulonDB)

Manual annotation of poorly defined/ambiguous amplicons

• Gene_Operon_mapping_Ecoli_K12_MG1655_U00096.3.csv - Feature-Amplicon matches
• Gene_Operon_mapping_Ecoli_K12_MG1655_U00096.3_numbered.csv - Feature-Amplicon matches
• Gene_Operon_mapping_Ecoli_K12_MG1655_U00096.3_numbered_remove.csv - Feature-Amplicon matches that need to be removed

Results files

• Amplicons_Ecoli_K12_MG1655_U00096.3.csv - Promoter region amplicons based on primer sequences provided in Zaslaver et al. 2006
• UAL_reannotated.csv - All info
• UAL_reannotated_multiple_reporting.csv - All info with multiple gene reporting
• UAL_reannotated_unique.csv - All info with unique gene reporting