|
| Status |
Public on Feb 05, 2021 |
| Title |
TCR-3: deletion of TCR |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Mycobacterium tuberculosis variant bovis |
| Characteristics |
tissue: Exponentially growing bacterial culture
genotype: deletion of TCR
|
| Growth protocol |
Exponentially growing bacterial cultures (OD600 0.4-0.6) were pelleted and washed once with 7H9/Tween-80
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from wild-type and mutant strains using TRIzol reagent (Invitrogen), followed by DNase I treatment.
Approximately 1-μg total RNA samples were treated by the Ribo-Zero rRNA removal procedure (Illumina) to enrichment for mRNA.
Approximately 1μg of RNA was used for library preparation using a ScriptSeq (v2) RNA-seq kit and high-throughput sequencing on an Illumina NextSeq platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
All raw sequence reads by RNA-Seq were initially pre-processed by Trimmomatic (v0.36) to trim the adaptor sequences and remove low-quality sequences.
The alignment results were input into Cufflinks (v2.2.1). Unless otherwise stated, the unit of expression level in our analyses is FPKM.
Cuffdiff (v2.2.1) was used to test for differential expression. We defined genes as differentially expressed using the following criteria: FPKM > 10 and FDR < 0.001. The data for visualization was generated by R (R Development Core Team, Vienna, Austria).
Supplementary_files_format_and_content: Table S2 Differential gene expression between wild type and the ΔTCR mutant
|
| |
|
| Submission date |
Feb 04, 2021 |
| Last update date |
Feb 05, 2021 |
| Contact name |
siyuan feng |
| E-mail(s) |
fsy3224502@gmail.com
|
| Organization name |
Sun Yat-Sen University
|
| Street address |
74 zhongshan 2nd road
|
| City |
Guang zhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL29695 |
| Series (1) |
| GSE166137 |
The involvement of Mycobacterium type III-A CRISPR-Cas system in oxidative stress and intracellular fitness |
|
| Relations |
| BioSample |
SAMN17776251 |
| SRA |
SRX10020378 |
