|
Status |
Public on Jun 09, 2023 |
Title |
CFP, rep1 |
Sample type |
SRA |
|
|
Source name |
extracellular cell-free pellet
|
Organism |
Apilactobacillus kunkeei |
Characteristics |
tissue: extracellular cell-free pellet cell type: gram-positive strain: A1401 treatment: none
|
Treatment protocol |
Cell suspensions were pelleted by centrifugation, the supernatant was filtered and ultracentrifuged to obtain the cell-free pellet (CFP), the pellet was washed to further obtain the Whole-cell lysate
|
Growth protocol |
The A. kunkeei strain and A1401 was cultivated in MRS-medium (Sigma Aldrich) according to (De Man et al., 1960) supplemented with 0.5% (w/v) D-Fructose (Sigma Aldrich) and 0.1% (v/v) Tween-80 (Sigma Aldrich), in the following referred to as fMRS. Batch-cultivation was performed at 35°C and 5% CO2 in batch-cultures of 100–150 mL fMRS medium and the cells were harvested during exponential growth phase at OD600 ≈ 0.3.
|
Extracted molecule |
total RNA |
Extraction protocol |
The RNA extraction was performed using the RiboPure-Bacteria Kit including DNAse I treatment (LifeTechnologies) Sequencing libraries were prepared from 500 ng total RNA using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, cat#20040525).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina MiSeq |
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|
Description |
CFP1.raw/CFP1 RNAseq.raw.read.counts.csv RNAseq.DESeq2.csv
|
Data processing |
read mapping using hisat2 v2.2.1 read quantification using FeatureCounts v2.0.1 Differential analysis with DESEq2 Assembly: A1401.gff, in-house genome assembly Supplementary files format and content: RNAseq.raw.read.counts.csv; raw read counts after mapping with hisat and read counting with featurecounts; columns: locus tag, gene length, feature, raw read counts for 6 samples, mean read counts for CFP and WCL group, gene length adjusted mean read counts for CFP and WCL group Supplementary files format and content: RNAseq.DESeq2.csv; read counts from DESeq2 and additional information for data analysis; columns: locus tag; log2-ratio (CFP vs WCL); raw and adjusted p-values; gene length; feature; normalized and corrected read counts from DESeq2; mean read counts for for CFP and WCL group; gene length adjusted mean read counts for CFP and WCL group; type of enrichment based on DESeq2 (adjusted p-value < 0.05, absolut log2-ratio > 1); genomic position; annotation; COG cateogry; COG family; prediction of signal peptides; prediction of transmembrane domains and signal peptides by Phobius
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Submission date |
Jun 13, 2022 |
Last update date |
Jun 09, 2023 |
Contact name |
Siv Andersson |
E-mail(s) |
siv.andersson@icm.uu.se
|
Organization name |
Uppsala University
|
Street address |
Husargatan 3
|
City |
Uppsala |
ZIP/Postal code |
752 37 |
Country |
Sweden |
|
|
Platform ID |
GPL32344 |
Series (1) |
GSE205998 |
Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles |
|
Relations |
BioSample |
SAMN29011455 |
SRA |
SRX15686246 |