|
| Status |
Public on Apr 18, 2024 |
| Title |
Mutant strain, iron deplete, 30 minutes, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
MAP3773c deletion strain
|
| Organism |
Mycobacterium avium subsp. paratuberculosis |
| Characteristics |
strain: MAP3773c deletion strain
treatment/time: Iron restriction post 30 minutes
|
| Treatment protocol |
Iron starvation was accomplished by treating cultures with DIP (200μM final) for 5, 30, 60, and 90 minutes shaken at 200rpm at 37°C
|
| Growth protocol |
Both strains were grown and maintained at 37°C in Middlebrook 7H9 broth supplemented with 10% OADC (oleic acid, dextrose, catalase); 0.05% Tween 80 and 2 mg/ml of ferric mycobactin J.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent followed by adding cholorform followed by centrifugation. The upper aqueous phase was added to a new microcentrifuge tube containing 100% RNase free ethanol which was then processed by Qiagen RNeasy kit DNase treatment and finally with the Ambion Turbo DNA-free kit.
RNA-Seq libraries were prepared using the mRNA Seq paired end read library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
M2_1
|
| Data processing |
All reads were checked for QC using FastQC (version 0.11.7) to visualize the quality of the reads using HPCC clusters.
Reads were processed using Trimmomatic tool to trim adaptor sequences/ low quality sequences using HPCC clusters.
Trimmed reads were mapped to reference genome (MAP K-10) using HISAT2. Reads counts were generated using HTSeq.
Assembly: MAP K-10 (Genbank accession number: NC_002944.2)
Supplementary files format and content: compressed gzip fastq files includes raw reads for each sample
Supplementary files format and content: tab-delimited text file include Normalised counts for each sample and replicates
|
| |
|
| Submission date |
Oct 05, 2023 |
| Last update date |
Apr 18, 2024 |
| Contact name |
Srinand Sreevatsan |
| E-mail(s) |
sreevats@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Pathobiology and Diagnostic investigation
|
| Street address |
784 WILSON RD
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL33823 |
| Series (1) |
| GSE244734 |
The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation |
|
| Relations |
| BioSample |
SAMN37700078 |
| SRA |
SRX22005973 |
