|
| Status |
Public on Oct 05, 2020 |
| Title |
RNA-Sequencing VapC21 deletion Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Microbe
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: Erdman
genotype/variation: VapC21 deletion
|
| Growth protocol |
For overexpression studies, early log phase cultures were induced were anhydrotetracycline addition for 24 hrs. For deletion strains, total RNA was isolated from mid log phase culture grown in 7H9 media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy minikit.
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 |
Data was subjected to quality control check by FastQC_v0.11.8
Reads were mapped to H37Rv and Erdman genome by TopHat v2.1.1
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Genome_build: ASM19595v2 (H37Rv) and ASM35020v1 (Erdman)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for VapC21 overexpression study.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for VapC21 deletion study.
|
| |
|
| Submission date |
Jul 13, 2020 |
| Last update date |
Oct 05, 2020 |
| Contact name |
Munmun Bhasin |
| E-mail(s) |
bhasin.munmun@gmail.com
|
| Organization name |
Indian Institute of Science
|
| Department |
Molecular Biophysics Unit
|
| Street address |
CV Raman Rd
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560012 |
| Country |
India |
| |
|
| Platform ID |
GPL18768 |
| Series (1) |
| GSE154320 |
Transcriptome analysis of VapC21 overexpression and deletion in Mycobacterium tuberculosis. |
|
| Relations |
| BioSample |
SAMN15518359 |
| SRA |
SRX8720507 |
