|
| Status |
Public on Oct 19, 2022 |
| Title |
Enterococci recovered from colonies grown 48h on MOLP_2 |
| Sample type |
SRA |
| |
|
| Source name |
48h
|
| Organism |
Enterococcus faecalis OG1RF |
| Characteristics |
tissue: 48h
genotype: Wild type
treatment: Surface penetration assay
|
| Treatment protocol |
Agar-penetrating (inside) and non-penetrating (outside) bacteria were collected post-inoculation at the indicated time points
|
| Growth protocol |
Bacteria were grown on semisolid MOLP agar plates for 24, 48, and 72h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were procesessed as described in Ramos, et al. 2022
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Out48_2
|
| Data processing |
bioinformatic analyses were conducted at LC Sciences bioinformatic services.
Reads were filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
Reads of all samples were aligned to the E. faecalis OG1RF reference genome using HISAT2 and then using UMI-tools sequence-deoendent bias and amplification noise were removed.
Assembly: The mapped reads were assembled using StringTie and merged using perl scripts and gff compare. Differential gene expression was determined using StringTie by calculating FPKM.
Supplementary files format and content: The excel file include FPKM values for each sample
|
| |
|
| Submission date |
Aug 26, 2022 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Diana K. Morales |
| E-mail(s) |
dim2018@med.cornell.edu
|
| Phone |
2127460451
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Obstetrics and Gynecology
|
| Street address |
1300 York Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL32603 |
| Series (1) |
| GSE212145 |
Transcriptional Profiling of Enterococcus faecalis During Surface Penetration |
|
| Relations |
| BioSample |
SAMN30526044 |
| SRA |
SRX17232119 |
