|
| Status |
Public on Jan 14, 2022 |
| Title |
H15 |
| Sample type |
SRA |
| |
|
| Source name |
lung tissue
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
tissue source: human lung
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by phenol- chloroform extraction and cell disruption by with Bead Beater (BioSpec Products, USA) as described (Rustad et al., 2009) and treated with Turbo DNase (Life Technologies, USA) to remove traces of genomic DNA.
RNA samples were depleted of both human and bacterial rRNA using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat), NEBNext® rRNA Depletion Kit (Bacteria) and polyA-transcripts using NEBNext® Poly(A) mRNA Magnetic Isolation Module. Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, USA) according to the manufacturers’ protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads were mapped to M.tuberculosis genome using bowtie2 v2.3.4.3 with parameters -p 4 --local --dovetail
Fragments counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of fragments overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped, non-chimeric fragments were used. The files "Counts_HXX.txt" represent these counts (File "Counts_all.csv" contains values for all samples).
Genome_build: AL123456.3
Supplementary_files_format_and_content: Counts - the numbers of overlapping reads for every annotated gene in each sample
|
| |
|
| Submission date |
Jan 12, 2022 |
| Last update date |
Jan 14, 2022 |
| Contact name |
Artem Grigorov |
| E-mail(s) |
[email protected]
|
| Organization name |
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
|
| Department |
Genomics and Postgenomic Technologies
|
| Lab |
Regulatory Transcriptomics
|
| Street address |
Ulitsa Miklukho-Maklaya, 16/10
|
| City |
Moscow |
| ZIP/Postal code |
117997 |
| Country |
Russia |
| |
|
| Platform ID |
GPL27507 |
| Series (1) |
| GSE193527 |
Transcriptomic profiling of M. tuberculosis from human lung tissue |
|
| Relations |
| BioSample |
SAMN24893602 |
| SRA |
SRX13748037 |
