|
| Status |
Public on Apr 15, 2014 |
| Title |
Fermentation 1- NAG 45 min |
| Sample type |
SRA |
| |
|
| Source name |
cells cultured in Bioreactors
|
| Organism |
Saccharopolyspora erythraea |
| Characteristics |
strain: NRRL2338
growth protocol: fermentation (cells cultured in bioreactor) - extraction after 45 mins of NAG induction
|
| Treatment protocol |
RNA isolation was performed after 8h incubation at 4C in RNA later (Ambion).
|
| Growth protocol |
Bioreactor fermentation using MM-101 chemically defined media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using two cycles of cellular lysis in Rnase-free zirconia beads, followed by column purifications using Qiagen RNAeasy.
Libraries were prepared using DSN treatment, following of mRNA enrichment using MicrobExpress (Ambion)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
E7007-4
|
| Data processing |
The initial image processing and base calling was done by a standard Software pipeline provided by Illumina. Reads were aligned to the S. erythraea genome using Burrows-Wheeler Aligner BWA and Bowtie requiring no more than 2 mismatches. Only reads that aligned to one genomic location were retained unless specified for the analysis. We employed CuffDiff to determine gene expression using SAM files resulting from alignment, annotated gene file, upper quantile normalization and masking of rRNA sequences.
Gene expression was normalized between the seven libraries for total alignable reads.
Genome_build: ASM6288v1
|
| |
|
| Submission date |
Apr 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Cuauhtemoc Licona-Cassani |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Queensland
|
| Department |
Australian Institute for Bioengineering and Nanotechnology
|
| Lab |
Centre for Systems and Synthetic Biotechnology
|
| Street address |
Crn College and Cooper rds
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL15864 |
| Series (1) |
| GSE56541 |
Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea |
|
| Relations |
| BioSample |
SAMN02720891 |
| SRA |
SRX512205 |
