|
| Status |
Public on Dec 29, 2012 |
| Title |
∆sigH mutant-Control-mRNA |
| Sample type |
SRA |
| |
|
| Source name |
∆sigH mutant-Control-mRNA
|
| Organism |
Mycobacterium avium subsp. paratuberculosis K-10 |
| Characteristics |
genotype/variation: delta-sigH mutant
strain: K-10
|
| Treatment protocol |
M. paratuberculosis cultures from mid-log phase were exposed to 10 mM diamide for 3 h. Control cultures were not treated with diamide.
|
| Growth protocol |
M. paratuberculosis strains were grown in Middlebrook 7H9 broth supplemented with 0.5% glycerol, 2 µg/ml mycobactin J and 10% ADC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol regent (Invitrogen)
Libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq RNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence. Raw RNA-seq data files in FASTQ format were assembled against the standard M. paratuberculosis K10 using the CLC Genomics Workbench 4.8 (CLC bio, Aarhus, Denmark). Gene expression for each of the different sample conditions was calculated using “reads per kilobase million” (RPKM) expression values (Mortazavi et al., 2008). The following formula was used to determine the RPKM values:
RPKM = Number of Reads/ (Kilobase length of gene × Millions mapped reads)
This RPKM metric enables comparisons between datasets with a varying number of total reads. All reads mapping to annotated non-coding RNA (ncRNA) were removed from the datasets before determining RPKM values. Datasets were quantile normalized and Kal’s Z-test (Kal et al., 1999) was used for the comparative gene expression analysis. Genes were considered significantly, differentially expressed if they showed ± 2.5 fold of change with FDR-P values < 0.05.
Genome_build: SRR060191 (http://www.ncbi.nlm.nih.gov/sra/?term=SRR060191). J. Bacteriol. December 2010 vol. 192 no. 23 6319-6320.
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Pallab Ghosh |
| E-mail(s) |
[email protected]
|
| Organization name |
UW-Madison
|
| Street address |
1656 Linden Dr
|
| City |
Madison |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL16429 |
| Series (1) |
| GSE43182 |
The Intracellular Life of Mycobacterium avium subsp. paratuberculosis During Macrophage Stress: A Key Role for the Alternative Sigma Factor, SigH |
|
| Relations |
| SRA |
SRX213163 |
| BioSample |
SAMN01881273 |
