|
| Status |
Public on Oct 07, 2020 |
| Title |
delcydAB-C-6_1 |
| Sample type |
SRA |
| |
|
| Source name |
H37Rv∆cydAB at T6, treated with combined,biological rep 1
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
genotype: H37Rv<delta>cydAB
condition: Q203 + ND-011992
time: 6 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Culure samples were collected and pelleted via centrifugation. Cell pellets were resuspended in Trizol reagent and RNA was harvested via phenol-chloroform extraction. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina reads were mapped to reference genome using bowtie2, which generated SAM files
SAM files were converted to coordinate-sorted BAM files using samtools
Reads per gene were countedusing featureCounts
Differential gene expression analysis was performed using DeSeq2
Data analysis protocol can be found in more detail in Benjak, et. Al., Methods Mol Biol, 2015
Genome_build: NC_000962.3
Supplementary_files_format_and_content: count files were produced from illumina fastq readfiles using fetureCounts and contain a raw count of reads per gene; DGE Analysis files were generated using DeSeq2 and contain analyzed read count comparisons between samples at time of starvation compared to time 0 (before starvation), these include p-values.
|
| |
|
| Submission date |
Oct 06, 2020 |
| Last update date |
Oct 09, 2020 |
| Contact name |
Erik James Hasenoehrl |
| E-mail(s) |
erik.hasenoehrl@gmail.com
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Microbiology & Immunology
|
| Lab |
Berney Lab
|
| Street address |
1301 Morris Park Ave. Price 569
|
| City |
Bronx |
| State/province |
New York |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL25498 |
| Series (1) |
| GSE159080 |
Transcriptional response of Mycobacterium tuberculosis to inhibition of Cytochrome bd oxidase and Cytochrome bcc:aa3 oxidase |
|
| Relations |
| BioSample |
SAMN16379330 |
| SRA |
SRX9249328 |
