|
| Status |
Public on Feb 22, 2023 |
| Title |
S7: MIX1443 day 3 (codon optimized) |
| Sample type |
SRA |
| |
|
| Source name |
prsA-je1zyn
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
genotype: prsA-je1zyn
experimental group: codon optimized
|
| Growth protocol |
B. subtilis strain 168 ΔspoIIAC ΔamyE Δapr ΔnprE ΔsrfAC was maintained on LBPG medium at room temperature and not placed at 4 C. Two different substrains were generated, one with a codon-optimized α-amylase JE1 sequence (prsA+je1zyn), and one with the wild-type sequence (prsA+je1). The genomic sequences for both substrains were retrieved in a separate experiment by Novozymes A/S. If not indicated otherwise, strains were cultivated at 37 C in erythromycin (1 µg/ml)-supplemented triptone-yeast (TY) medium when appropriate. The bacterial enzyme production fermentations were conducted in duplicates in custom Novozymes made 5L tanks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were harvested by mixing 5 ml cell culture with 5 ml 100% ethanol, immediately storing on dry ice before transferring to -80°C. RNA was isolated using phenol-chloroform extraction.
Bacterial RNA library preparation was prepared from rRNA-depleted total RNA as described in https://doi.org/10.1002/cpnc.55
Single-end sequencing on an Illumina NextSeq 500. The read lengths were 76 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MIX1443 day 3 (codon optimized)
|
| Data processing |
QC with FastQC and trimmomatic
PCR bias reduction with Bbmap (first 7 bases of reads)
Mapping with segemehl
Identification of potential novel ncRNA with ANNOgesic + custom script
Expression analysis with featureCounts
Genome_build: (proprieatary genome sequence, part of bioproject)
Supplementary_files_format_and_content: DESeq2 normalized expressions
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Feb 22, 2023 |
| Contact name |
Christian Anthon |
| E-mail(s) |
anthon@rth.dk
|
| Phone |
+4521510929
|
| Organization name |
University of Copenhagen
|
| Department |
Veterinary and Animal Sciences
|
| Lab |
RTH
|
| Street address |
Thorvaldsens Vej 57
|
| City |
Frederiksberg C |
| ZIP/Postal code |
1871 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL21796 |
| Series (1) |
| GSE179570 |
CRISPRi screen for a-amylase yield improvements in Bacillus subtilis |
|
| Relations |
| BioSample |
SAMN20081579 |
| SRA |
SRX11362046 |
