|
| Status |
Public on Apr 01, 2020 |
| Title |
Wild type rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro aerobic culture of the wild type strain
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
strain background: MC2 155
genotype/variation: wild type
conditions: in vitro
|
| Growth protocol |
The M. smegmatis strains were grown aerobically in Middlebrook 7H9 medium supplemented with 0.2% glucose and 0.02% Tween 80 (vol/vol) on a gyratory shaker (200 rpm) at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The stains were grown until an optical density at 600 nm reached 0.45 to 0.5. Cells were harvested by centrifugation at 4°C with 3500×g for 3 min. The cell pellets were resuspended with 1 ml TRIzol (Invitrogen). Procedures of total RNA extract from the cell pellets were performed using TRIZol purchased from Invitrogen and followed the instructions provided to users.
Six ibraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Using FASTX-Toolkit, raw data derived from RNA-seq was filtered to a minimum phred quality score of 28.
The BWA-MEM algorithm was employed to align the filtered reads into the reference genome.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bam2readcount.
Counted values were nomalised in the RPKM method.
Genome_build: Mycobacterium smegmatis MC2 155 ASM1500v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 10, 2017 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Jungwook Park |
| E-mail(s) |
[email protected]
|
| Organization name |
Pusan National University
|
| Department |
Microbiology
|
| Street address |
Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea
|
| City |
Busan |
| ZIP/Postal code |
ASI|KR|KS012|PUSAN |
| Country |
South Korea |
| |
|
| Platform ID |
GPL23277 |
| Series (1) |
| GSE97620 |
RNA deep sequencing data of the whole transcriptomes of the wild-type and furA triple mutant strains of Mycobacterium smegmatis MC2 155 |
|
| Relations |
| BioSample |
SAMN06706503 |
| SRA |
SRX2732362 |
