|
| Status |
Public on Feb 28, 2023 |
| Title |
Bt_HD73_pCER_plus_LB_biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
liquid bacterial culture
|
| Organism |
Bacillus thuringiensis |
| Characteristics |
strain: HD73
tissue: liquid bacterial culture
time: Early stationary phase
genotype: pAW63{delta}; pCER270+
medium: LB
|
| Growth protocol |
For RNA preparation, LB cultures were collected two hours (early stationary phase) after the beginning of stationary phase, whereas in HCT medium the cultures were collected four hours after the onset of the stationary phase (commitment to sporulation). The onset of the stationary phase is determined as the end of the exponential growth and corresponds to an inflection of the growth curve.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using Trizol and 1-bromo-3-chloropropane
After ribosomal RNA depletion, NextSeq 500/550 High Output Kit v2 was used to construct library
Single-read 75 sequencing run
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Demultiplexing using bcl2fastq2-2.18.12
Adaptors trimming with Cutadapt 3.2
Read alignment to references genome with Bowtie2 in Galaxy. Write unaligned reads (in fastq format) to separate file(s): False; Write aligned reads (in fastq format) to separate file(s): False; Do you want to set paired-end options?: no Will you select a reference genome from your history or use a built-in index?: indexed; Select reference genome: internal genomes uploaded from NCBI; Set read groups information?: do_not_set; Select analysis mode: simple; Do you want to use presets?: Very fast end-to-end (--very-fast); Save the bowtie2 mapping statistics to the history: True
Read counting with MulticovBed in Galaxy. Calculation based on strandedness?: Only overlaps occurring on the **same** strand.; minimum overlap required as a fraction of A: 1e-09; Require that the fraction of overlap be reciprocal for A and B: False; Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage: False; Minimum mapping quality (MAPQ) allowed:0; Include duplicate reads: True; Include failed-QC reads: False; Only count proper pairs: False
CP001179 (pCER270); CP001177 (Chromosome) and CP001178-CP001181 (plasmids) for AH187 = Bc_F4810-72; CP004069 (Chromosome) and CP004069-CP004076 (plasmids) excluding CP004072 (pAW63) for B_th_HD73; in-house unpublished genome for B_we_KBABA6
Supplementary files format and content: raw count txt files
Supplementary files format and content: BweKBAB6_pXO16tcR_corrV170303.txt is a file with FASTA sequences corresponding to each transcriptional feature
|
| |
|
| Submission date |
Dec 12, 2022 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Alicia Nevers |
| E-mail(s) |
alicia.chery@gmail.com
|
| Organization name |
Institut national de la recherche agronomique (Inrae)
|
| Department |
Micalis
|
| Lab |
Microbial Genetics and Environment
|
| Street address |
Domaine de Vilvert
|
| City |
JOUY-EN-JOSAS |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL32378 |
| Series (1) |
| GSE220688 |
Impact of pCER270 on Bacillus cereus sensu lato gene expression |
|
| Relations |
| BioSample |
SAMN32163736 |
| SRA |
SRX18643943 |
