|
| Status |
Public on Feb 20, 2015 |
| Title |
RV1026 knock-down 2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Mycobacterium tuberculosis CDC1551 |
| Characteristics |
strain: CDC1551
treatment: RV1026 knock-down
|
| Growth protocol |
The logarithmically growing cultures (O.D.= 0.5) of the Rv1026 knock-down, ppk1 knock-in, and empty vector control strains
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol-based methods
RNA libraries were prepared by standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mid log growth stage (OD 0.5)
|
| Data processing |
The sequence quality of the datasets was checked by fastQC software
The RNA-seq data were aligned with the CDC1551 genome obtained from Ensembl (bacteria, http://bacteria.ensembl.org) using bowtie2
HTSeq-count script written in python was used to obtain the read counts of each CDC1551 gene from the SAM alignment file.
The GTF annotation file from the bacterial Ensembl website was used during read counting for gene annotation. Since the library was strand-specific, HTSeq was employed with appropriate configurations (default). Normalization and analysis of differential expression were performed using DEseq2 package of bioconductor.
Genome_build: n/a
Supplementary_files_format_and_content: genes and counts
|
| |
|
| Submission date |
May 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu-Min Chuang |
| E-mail(s) |
yu-min.chuang@yale.edu
|
| Organization name |
Yale University
|
| Department |
Infectious disease
|
| Street address |
1 Gilbert St TAC S410
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL18715 |
| Series (1) |
| GSE57868 |
Accumulation of inorganic polyphosphate mediates metabolic downshift and antibiotic tolerance in Mycobacterium tuberculosis |
|
| Relations |
| BioSample |
SAMN02796377 |
| SRA |
SRX548840 |
