|
| Status |
Public on Jun 27, 2021 |
| Title |
IBUN13A Gly3 |
| Sample type |
SRA |
| |
|
| Source name |
IBUN13A grown on Glycerol
|
| Organism |
Clostridium sp. IBUN13A |
| Characteristics |
strain: IBUN13A
genotype: wild type
treatment: grown on Glycerol
|
| Growth protocol |
Microorganism was grown on an industrial culture media containing 40 g/L of glyerol or 20 g/L of glucose, under anaerobic conditions at 35 +/- 2°C for 24 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pellets from 40 mL culture vessels were collected and the procedures from TRIzol® Max™ Bacterial RNA Isolation Kit and RNeasy Protect Bacteria Mini Kit de Qiagen ® were followed
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina TruSeq stranded mRNA (microbe)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence trimming and filtering was performed using BBDuk2 using standard parameters and SILVA 16SrRNA database, and quality evaluation was done using FastQC
To determine transcripts abundance, genome sequence of Clostridium sp. IBUN13A previously obtained (JZWG00000000) and Kallisto 0.46.0 were used.
Differential expression was determined using Bioconductor's DESeq2 , taking into account log2 ratio ≥1,5 and adjusted p value equal or less than 0,1
Genome_build: Accesion no. JZWG00000000
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 26, 2021 |
| Last update date |
Jun 27, 2021 |
| Contact name |
Ximena Carolina Perez-Mancilla |
| E-mail(s) |
xcperezm@unal.edu.co
|
| Organization name |
Universidad Nacional de Colombia
|
| Street address |
Cra 30 #45 - 03
|
| City |
Bogotá D.C. |
| ZIP/Postal code |
111321 |
| Country |
Colombia |
| |
|
| Platform ID |
GPL30317 |
| Series (1) |
| GSE178968 |
Transcriptomic insights of a 1,3-Propanediol producer Clostridium strain isolated from Colombian soil |
|
| Relations |
| BioSample |
SAMN19895499 |
| SRA |
SRX11234304 |
