|
| Status |
Public on Jul 31, 2023 |
| Title |
3SL 2% B.breve midlog growth 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Bifidobacterium breve |
| Characteristics |
tissue: bacterial cells
treatment: 3SL
|
| Treatment protocol |
Three different carbon sources as energy - Lactose, 3SL or BMO
|
| Growth protocol |
Grown in the anaerobic hood at 37 degrees celcius. Growth media is basal MRS and 2% Lactose or 3SL or BMO as the energy source
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected to RNA protect and Qiagen RNA easy kit was used. Before Qiagen protocol Mutanolysin and Protnase K was used.to open the cells
Ribodepletion was conducted using RiboZero plus kit and illumina prokaryotic RNA seq library was constructed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequence files were uploaded in to CLC genomic work bench 12.0 (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-genomics-workbench/). Data quality was checked and then the RNAseq analysis was conducted by aligining the sequence read in to to the genome of B. breve 1107E in CLC genomic work bench.
Assembly: B. breve SW 1107E genome is deposited in the JGI/IMG database and will be released upon manuscript submission.
Supplementary files format and content: Processed files are obtained from CLC genomic work bench and each file was exported as tab limited txt file. Processed files cotain the gene ID and the expression in RPKM
|
| |
|
| Submission date |
Jul 11, 2023 |
| Last update date |
Jul 31, 2023 |
| Contact name |
David A Mills |
| E-mail(s) |
damills@ucdavis.edu
|
| Phone |
5307547821
|
| Organization name |
University of California Davis
|
| Department |
Dept. of Food Science and Technology
|
| Lab |
1221 RMI South
|
| Street address |
One Shields ave
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL33564 |
| Series (1) |
| GSE237076 |
Gene expression in B breve SW1107E in the presence of media containing lactose, BMO and 3SL as carbon sources |
|
| Relations |
| BioSample |
SAMN36407771 |
| SRA |
SRX20985185 |
