|
| Status |
Public on Mar 04, 2019 |
| Title |
06-mtb-BMDM-inf-2h-RNA-seq_C |
| Sample type |
SRA |
| |
|
| Source name |
M. tuberculosis infected BMDMs
|
| Organisms |
Mycobacterium tuberculosis; Mus musculus |
| Characteristics |
strain: M. tuberculosis H37Rv and M. musculus C57BL/6 mice
tissue: M. tuberculosis infected BMDMs
genotype: wildtype
age: 2 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer (QBiogene) three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using the Direct-zol RNA MicroPrep kit (Zymol Research) according to manufacturer’s instruction with on-column DNase treatment. Total RNA was depleted of rRNA using Illumina RiboZero Gold Epidemiology kit.
RNA libraries for Path-seq were prepared using the SureSelectXT strand-specific RNA target enrichment for Illumina multiplexed sequencing using custom MTB probes (assembly M_tub_h37rv_ASM19595v2_32_1). RNA libraries for RNA-seq were prepared using the SureSelectXT strand-specific RNA kit, but were not hybridized to probes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
infected, standard RNA-seq
|
| Data processing |
Raw FASTQ read data were processed using the R package DuffyNGS
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2 and Mus Musculus GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files includes RPKM and read countss for each sample, meta-data (time and dissolved oxygen for each sample)
|
| |
|
| Submission date |
Jun 27, 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 |
GPL25252 |
| Series (1) |
| GSE116357 |
Active Mycobacterium tuberculosis regulatory networks from in vitro infection of mouse macrophages uncovered by Path-seq |
|
| Relations |
| BioSample |
SAMN09503043 |
| SRA |
SRX4314639 |
