|
| Status |
Public on Feb 22, 2013 |
| Title |
GCK_induced_PYRENE |
| Sample type |
SRA |
| |
|
| Source name |
Prokaryotic cell contents
|
| Organism |
Mycolicibacterium gilvum PYR-GCK |
| Characteristics |
strain: PYR-GCK
protocol: induced_PYRENE
|
| Treatment protocol |
separate supplements of 25mM pyrene substrate and 0.38g/L D-glucose substrate (supplements identified as induced and control in analyzed data, respectively)
|
| Growth protocol |
Cultivation in 200ml defined minimal media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNAiso reagent and 45 seconds bead-beating. mRNA enrichment with Ribo-Zero rRNA removal kit. Illumina TruSeq RNA Sample Prep Kit used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling
Data was treated with low-quality filtering using Prinseq 0.19.3.
Filtered reads were mapped with reference genome using Bowtie2 version 2.0.0, default option
Differential expression analysis using Cuffdiff in Cufflinks 2.0.2 package.
Genome_build: ASM1636v1; GenBank CP000656
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and statistical analysis of gene expression between control and induced samples
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Abimbola Comfort Badejo |
| Organization name |
Hanyang University
|
| Street address |
1271 Sa3dong
|
| City |
Ansan |
| ZIP/Postal code |
426-791 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16708 |
| Series (1) |
| GSE44536 |
A global differential transcriptomic profiling of Mycobacterium gilvum PYR-GCK during pyrene and glucose metabolism, using RNA seq. |
|
| Relations |
| SRA |
SRX243759 |
| BioSample |
SAMN01923918 |
