|
| Status |
Public on Mar 04, 2019 |
| Title |
MSMEG_0916_induced |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
strain: mc2155
genotype/variation: MSM pDTCF-MSMEG_0916 indcued
treated with: 100 ng/ml ATc
treatment time: 4 hour
|
| Treatment protocol |
induced sample treated with 100 ng/ml Atc for overexpression of MSMEG_0916
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Biological triplicate cultures of M. smegmatis containing pDTCF-MSMEG_0916 in 7H9 media, were grown as 50 mL cultures , at 37ºC, 5%CO2, for 4 hours in the presence or absence of 100 ng/ml anhydrotetracycline.
DNA libraries were prepared for sequencing using ThruPLEX DNA-seq Kit (Rubicon) standard protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
04-MSMEG0916-Atc_S4
|
| Data processing |
Samples were sequenced on the NextSeq sequencing instrument in mid output 150 v2 flow cell. Unpaired 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium smegmatis mc2155 ASM1500v1
Supplementary_files_format_and_content: csv file containing identified ChIP-peak with scores and significance as described in Minch et al (2015) Nature Communications.
|
| |
|
| Submission date |
Jun 20, 2018 |
| Last update date |
Mar 06, 2019 |
| Contact name |
Eliza Peterson |
| Organization name |
Institute for Systems Biology
|
| Lab |
Baliga
|
| Street address |
401 Terry Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL25202 |
| Series (2) |
| GSE116084 |
Path-seq identifies an essential mycolate remodeling program for mycobacterial adaptation in host cells [ChIP-seq] |
| GSE116085 |
An essential mycolate remodeling program for mycobacterial adaptation in host cells |
|
| Relations |
| BioSample |
SAMN09462613 |
| SRA |
SRX4277284 |
