|
| Status |
Public on Jul 20, 2019 |
| Title |
RNA-Seq of knockout of Rv1565c rep2 |
| Sample type |
SRA |
| |
|
| Source name |
in-vitro
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
parental-strain: H37Rv
genotype: Rv1565c KO
|
| Growth protocol |
Cultures were grown to log-phase in-vitro in 7H9 medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were bead-beat with trizol, and then DNA was extracted by ethanol precipitation.
Illumina RNA-seq sample prep protocol. Depletion of ribosomal RNA using Ribo-Zero kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAseq_Rv1565c_KO
|
| Data processing |
Samples were sequenced on an Illumina HiSeq 2500 Rapid in paired-end mode with 125+125bp read length.
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings.
Reads were mapped to the H37Rv genome use BWA 0.7.12. Read-counts in each ORF were tabulated and converted to RPKMs.
Analysis of differential expression for each knockout strain (compared to parental strain, H37Rv) was performed using DESeq2.
Genome_build: H37RvMA (GCA_000751615.1)
Supplementary_files_format_and_content: Counts files: *.expr files are tab-separated text files that contains abundances for each gene. 6 columns are: ORF id, gene name, length (bp), strain, number of reads mapping to ORF, RPKM.
Supplementary_files_format_and_content: DESeq2 output: tab-delimited files containing log-fold-change and significance (adjusted P-value) for each gene compared to wild-type (H37Rv).
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Jul 20, 2019 |
| Contact name |
Thomas R Ioerger |
| E-mail(s) |
ioerger@cs.tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
Department of Computer Science
|
| Street address |
3112 TAMUS
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843-3112 |
| Country |
USA |
| |
|
| Platform ID |
GPL17879 |
| Series (1) |
| GSE134574 |
Transcriptomic analysis of gene-knockouts in M. tuberuclosis H37Rv |
|
| Relations |
| BioSample |
SAMN10654100 |
| SRA |
SRX5183303 |
