Barcoded overexpression screens in gut Bacteroidales identify genes with new roles in carbon utilization and stress resistance"

Data downloads for "Barcoded overexpression screens in gut Bacteroidales identify genes with new roles in carbon utilization and stress resistance"
genomes.tar.gz includes the genomes and annotations for Bacteroides thetaiotaomicron VPI-5482 and for the six other source organisms. orgId.names explains which assembly identifier goes with which insert library.
mapping_*.tar.gz has the final results of the mapping script, with the 05-BC_and_genes_dfs subdirectory for each library.
The scripts for mapping are in Boba-seq.tar.gz
Also see
https://github.com/OGalOz/Boba-seq
(which may have an updated version)
bobaseq.R has the R functions for computing strain fitness values and identifying statistically significant and biologically consistent hits. Also see
https://github.com/morgannprice/BobaseqFitness
(which may have an updated version of the script)
fit2.R has the commands to build the R image, using the routines in bobaseq.R
Btcomb.image has the resulting R image.
bobaseq_figs.R has R commands for making the figures.
The Boba-seq samples are described in Bt_bobaseq_exps_2023Sep11.tsv
faa.hits has the results of all-versus-all protein similarity (from blastp) for these 7 genomes. Also see psim in the R image. These are used to help identify biologically consistent hits.
The *.gb files are vector maps for pNBU2-repA1, pNBU2-repA2, and pNBU2-repA3, pNBU2-repA1-barcoded, pFD340, and pKSH24.
AH*.fq.gz are paired-end RNASeq data for B. thetaiotaomicron carrying two different plasmids with 3 replicates each. AH001, AH002, and AH003 are the empty vector samples. AH004, AH005, and AH006 are the samples with the ssb protein ("fragment 2") in the insert.