|
| Status |
Public on Dec 01, 2020 |
| Title |
LP_HMO_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria from human oral cavity
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
strain: ATCC BAA-793
treatment: pooled human milk oligosaccharides (HMO)
|
| Treatment protocol |
glucose, xyloglucans isolated from cranberries with or without two cranberry proanthocyanidin (PAC) extracts, human milk oligosaccharides with or without PACs, fructooligosaccharides with or without PACs, glucose and two extract of PACs alone
|
| Growth protocol |
Lactobacillus plantarum were routinely propagated in De Man Rogosa Sharp medium supplemented with 0.05 % (m/v) L-cysteine hydrochloride at 37°C under anaerobic conditions. Cells then transferred into 3 ml of modified MRS medium (no carbohydrate source). Carbohydrate source is replaced with either 1% w/v xyloglucans, human milk oligosaccharides, fructoligosaccharides, and glucose as the control. Two PAC fractions were added as 1 mg/ml and cells were grown till mid-log phase under same conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were suspended in lysis buffer in Lysing Matrix E beadbeating tubes to disrupt cell walls with a FastPrep 56624 bead beater. Bead beating was performed twice at 5.5 m/s for 30 seconds with a 1 min incubation on ice. The Ambion RNAqeous protocol was followed and terminated with total RNA elution into 50 μl of EB solution. Then, total RNA were treated for DNA removal. DNA-free extracts were subjected to ribosomal RNA depletion via the Ribo-Zero Magnetic Kit for bacteria and cleaned up with RNeasy MinElute Cleanup Kit. Purified mRNA was used asseses for quality and used for RNA-seq library preparation.
mRNA enriched library preparation was performed with the NEBNext Ultra II Directional kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence using trimmomatic, and masked for low-complexity or low-quality sequence, cleaned for 16S rRNA contamination using bbduk then mapped to L. plantarum WCFS1 whole genome using bowtie2 v2.3.4.3 with parameters -p 8
Aligned reads were then name sorted using Samtools (v1.4.1) and total and specific gene counts were obtained by overlapping to a specific genomic locus(i.e. locus tag) with genomic feature and annotation (GFF) using HTSeq (v0.10.0) with parameters --stranded=reverse --nonunique=all --mode=union --order=name .
Raw gene counts were subject to DEseq2 and log2 fold changes obtained for one condition relative to other
Genome_build: Lactobacillus plantarum WCFS1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Normalized differential expression as log2 fold change from DeSeq2
|
| |
|
| Submission date |
Oct 31, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Ezgi Ozcan |
| E-mail(s) |
eozcan@umass.edu
|
| Organization name |
University of Massachusetts Amherst
|
| Street address |
424 Chenoweth Lab, 102 Holdsworth Way
|
| City |
Amherst |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
01003 |
| Country |
USA |
| |
|
| Platform ID |
GPL29328 |
| Series (1) |
| GSE160565 |
Cranberry proanthocyanidins and dietary oligosaccharides synergistically modulate Lactobacillus plantarum physiology |
|
| Relations |
| BioSample |
SAMN16617455 |
| SRA |
SRX9411585 |
