|
| Status |
Public on Feb 08, 2019 |
| Title |
10293: rpoS KO (ACCM-D) 5d |
| Sample type |
SRA |
| |
|
| Source name |
ACCM-D axonic media
|
| Organism |
Coxiella burnetii |
| Characteristics |
strain: RSA493
genotype: rpoS knock out
|
| Growth protocol |
C. burnetii strains were inoculated into 20 ml of ACCM-D growth media at 1x105 GE/ml
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At days 5 and 14, RNA was extracted using a hot trizol extraction
Ribozero gram- --> Truseq mRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cb whole genome using bowtie
normalization and comparisons were run using deseq2, matrix_11s.txt is a condensed file of the original with deseq2 normalized reads for each sample listed
Genome_build: GCF_000007765.2 2016/11/10 (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Coxiella_burnetii/latest_assembly_versions/GCF_000007765.2_ASM776v2)
|
| |
|
| Submission date |
Feb 02, 2018 |
| Last update date |
Feb 08, 2019 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
[email protected]
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL24577 |
| Series (1) |
| GSE110091 |
RpoS regulates genes associated with development of the small cell variant developmental form of Coxiella burnetii |
|
| Relations |
| BioSample |
SAMN08457705 |
| SRA |
SRX3644319 |
