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| Status |
Public on Aug 31, 2020 |
| Title |
sync16; 1_55hr |
| Sample type |
SRA |
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| Source name |
in vitro thermal shift
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| Organism |
Mycobacterium tuberculosis |
| Characteristics |
genotype: dnaA cold-sensitive mutant (cos)
timepoint: 55hr
replicate: 1
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| Treatment protocol |
The cells were shifted to 30ºC for 36 hours. The cultures were then shifted to 37ºC and the cultures were processed for RNA isolation at the following times: 0h, 3h, 6.5h, 9h, 12h, 18.5h, 21h, 27h, 31h, 33h, 36h, 39.5h, 42h, 45.5h, 52h and 55h.
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| Growth protocol |
Cultures of Mtb H37Rv and dnaAcos115 (mutant strain generated in a previous study, Nair et al, 2009, Mol Micro, 71(2):291-304) were grown in standard culture media at 37ºC under shaking conditions till OD600 0.4.
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| Extracted molecule |
total RNA |
| Extraction protocol |
At each timepoint, 45ml culture was pelleted and resuspended in 1ml of TRIzol (Invitrogen) and transferred to lysing matrix tubes (MP Biomedicals: Lysing Matrix B). Cells were lysed in a MP Biomedicals Fast Prep-24 homogenizer (maximum power-6.5, 4 X 30s cycles, rest on ice for 5 minutes in between cycles). RNA was purified according to the manufacturer?s directions. RNA cleanup was performed with Qiagen RNeasy Mini kit 27 (74104) omitting the DNase step. Instead, after elution, in-tube DNase treatment was performed using Ambion DNase Turbo. RNeasy cleanup was repeated again with double volumes of RLT and ethanol. RNA was subjected to rRNA removal with Ribozero Bacteria kit (Illumina-MRZB12424).
Deep sequencing library was prepared using KAPA Stranded RNASeq kit (KK8401).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
sync16
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| Data processing |
The reads were mapped to the H37Rv genome using BWA (Burroughs Wheeler Aligner; Li and Durbin, 2009) with default parameter settings. Reads mapping to each ORF were totaled (sense-strand only). Because certain loci were over-represented (e.g. rrs, rnpB, ssr, Rv3661), with 0.5-1.0 million reads each, counts were truncated to a maximum coverage of 10,000 (reads/nt). Gene abundances were normalized across all timepoints and replicates using DESeq2 (Love, Huber, Anders, 2014).
Genome_build: NC_000962.3
Supplementary_files_format_and_content: total_deseq_norm.xlsx contains normalized gene abundances for all samples
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| Submission date |
Mar 22, 2020 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Thomas R Ioerger |
| E-mail(s) |
ioerger@cs.tamu.edu
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| Organization name |
Texas A&M University
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| Department |
Department of Computer Science
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| Street address |
3112 TAMUS
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| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843-3112 |
| Country |
USA |
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| Platform ID |
GPL25317 |
| Series (1) |
| GSE147345 |
Cell cycle-associated expression patterns predict gene function in mycobacteria |
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| Relations |
| BioSample |
SAMN14421875 |
| SRA |
SRX7966197 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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