|
| Status |
Public on Apr 27, 2016 |
| Title |
SF-10-48hr [RMB108] |
| Sample type |
SRA |
| |
|
| Source name |
cultured bacteria
|
| Organism |
Mycobacterium tuberculosis CDC1551 |
| Characteristics |
concentration: soluble fraction (SF) 10 ug/ml
time point: 48hour exposure
|
| Treatment protocol |
Bacterial cells were co-incubated with lysosomal soluble fraction at non-inhibitory (10 μg/ml SF, 24hrs), sub-inhibitory (10 μg/ml SF, 48hrs) and inhibitory (20 μg/ml SF, 48hrs)
|
| Growth protocol |
In vitro cultures of M. tuberculosis CDC1551 wildtype strain were grown to mid-log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Treated bacterial cells were treated with RNAprotect Bacteria reagent (Qiagen), followed by extraction of total RNA using RNeasy Minikit (Qiagen) according to the manufacturer’s instructions. rRNA was depleted with Ambion’s MICROBExpress Kit (AM1905) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina TRUseq version 2 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CDC1551 (NC_002755) whole genome using CLCgenomics workbench 6.5 with parameters: unspecific match limit = 10, additional upstream bases = 0, count paired reads as two = Yes, minimum exon coverage fraction = 0.2, minimum length fraction (long reads) = 0.9, minimum similarity fraction (long reads) = 0.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from CLC genomics workbench 6.5
Genome_build: ASM858v1; CDC1551 (NC002755)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Apr 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ahmad Nazri Mohamed Naim |
| E-mail(s) |
mohamedan@gis.a-star.edu.sg
|
| Phone |
65-98547654
|
| Organization name |
Genome institute of Singapore
|
| Department |
Infectious disease
|
| Lab |
lab 1
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20114 |
| Series (1) |
| GSE68337 |
A Lysosomal In Vitro Exposure (LivE) Model to Identify Pathways Critical for Mycobacterium tuberculosis Intracellular Persistence |
|
| Relations |
| BioSample |
SAMN03570397 |
| SRA |
SRX1012314 |
