Study of ColE1 expression using public data

Finding relevant data in short read archive

We searched {NCBI_SRA] (https://www.ncbi.nlm.nih.gov/sra) with the following query:

https://www.ncbi.nlm.nih.gov/sra?term=(((((%22escherichia%20coli%22%5BOrganism%5D)%20AND%20illumina%5BPlatform%5D))%20AND%20%22transcriptomic%22%5BSource%5D)%20AND%20%22rna%20seq%22%5BStrategy%5D)%20AND%20(%222018%22%5BPublication%20Date%5D%20%3A%20%222019%22%5BPublication%20Date%5D)

((((("escherichia coli"[Organism]) 
AND illumina[Platform])) 
AND "transcriptomic"[Source]) 
AND "rna seq"[Strategy]) 
AND ("2018"[Publication Date] : "2019"[Publication Date]) 

possible good hit: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA459526

This contaions 16 datasets, we downloaded RunInfo table from NCBI and removed columns to produce this:

Run download_path LibraryName SRR7119574 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119574 lacZ_ind_RPF_r2 SRR7119575 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119575 lacZ_ind_mRNA_r2 SRR7119576 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119576 lacZ_unind_RPF_r2 SRR7119577 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119577 lacZ_unind_mRNA_r2 SRR7119562 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119562 lacZ_ind_RPF_r1 SRR7119563 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119563 lacZ_ind_mRNA_r1 SRR7119572 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119572 lacZ_unind_RPF_r1 SRR7119573 https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006952/SRR7119573 lacZ_unind_mRNA_r1

Read processing

The reads contain the following adapters:

-a 
-b 
-g