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Sample GSM6238831 Query DataSets for GSM6238831
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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