|
| Status |
Public on May 31, 2021 |
| Title |
2FL_C |
| Sample type |
SRA |
| |
|
| Source name |
2FL_C
|
| Organism |
Bifidobacterium pseudocatenulatum |
| Characteristics |
strain: MP80
treatment: Grown on 2% 2'-FL
|
| Treatment protocol |
Treatment is MRS media supplemented with 2% 2'-FL or 2% LNFP1, control is MRA media supplemented with 2% lactose.
|
| Growth protocol |
Bifidobacterium pseudocatenulatum MP80 inoculated into basal MRS media supplemented with 2% lactose, 2% 2'-FL or 2% LNFP1 in four biological replicates, sample collection at mid log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cells were immediately pelleted and resuspended in 1ml of RNAprotect Bacteria Reagent. Cells were pre-lysed lysozyme and mutanolysin. Then, Total RNA is extracted using the RNeasy mini kit (Qiagen Inc, Valencia). Total RNA samples were DNase treated twice. Ribosomal RNA depletion was carried using RiboMinus Transcriptome Isolation Kit, bacteria (Thermo Fisher, Waltham, MA) on 1 μg of total RNA.
Barcode indexed RNA-seq libraries were generated from 20 ng ribo-depleted RNA using the Kapa Hyper Stranded RNA-seq kit (KapaBiosystems, Cape Town, South Africa).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DNase treated total RNA
ribo-depleted RNA
|
| Data processing |
Demultiplexed sequence files were processed using the CLC-Bio Genomics Workbench (CLC Bio, Denmark). Reads were trimmed (maximum of 2 ambiguous base pairs) and deleted if the quality scores were below 0.5.
Edited reads were aligned to fasta files generated for Bifidobacterium pseudocatenulatum MP80 genome at IMG.
Reads Per Kilobase per Million mapped reads (RPKM) values were automatically calculated by CLC-Bio Genomics Workbench by using information on the gene length, total and unique gene reads aligning to a specific locus tag.
Genome_build: Bifidobacterium pseudocatenulatum MP80 genome at IMG.
Supplementary_files_format_and_content: *.txt: Matrix tables with raw gene counts and RPKM for every gene and every sample.
|
| |
|
| Submission date |
May 30, 2021 |
| Last update date |
Jun 01, 2021 |
| Contact name |
saumya wickramasibnghe |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California Davis
|
| Department |
Food Science and Technology
|
| Lab |
Mills lab
|
| Street address |
One Shields AVE
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL30210 |
| Series (1) |
| GSE175820 |
RNA sequencing of Bifidobacterium pseudocatenulatum MP80 grown on Lactose 2'-FL and LNFP-1 |
|
| Relations |
| BioSample |
SAMN19459993 |
| SRA |
SRX11033799 |
