|
| Status |
Public on Mar 04, 2019 |
| Title |
02_uninfected_mtb_24h_B |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: M. tuberculosis H37Rv
tissue: bacterial culture
genotype: wildtype
age: 24 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 chloroform/isopropanol extraction method with 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 |
uninfected
|
| 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 counts for each sample.
|
| |
|
| Submission date |
Jun 28, 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 |
GPL22688 |
| Series (1) |
| GSE116394 |
Active Mycobacterium tuberculosis regulatory networks from alveolar macrophages of in vivo mouse infection uncovered by Path-seq |
|
| Relations |
| BioSample |
SAMN09514672 |
| SRA |
SRX4319040 |
