|
| Status |
Public on Jan 01, 2024 |
| Title |
12 hour post-infection 4 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow-derived macrophages
|
| Organism |
Mus musculus |
| Characteristics |
agent: Mycobacterium avium subsp. hominissuis (MAH) strain TH-135
time point: 12 hout post-infection
strain: BALB/c
cell type: Bone marrow-derived macrophages
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and lysed with 700 μl of Qiazol and stored at minus 80 oC for RNA extraction. Total RNA was prepared using miRNAeasy kit. RNA quality was assessed by Bioanalyzer to ensure that RIN (RNA integrity number) is over 7.0, and A260/280 and A260/230 ratios are over 1.7.
Transcriptome analysis was performed by CAGE. The CAGE libraries were constructed using the published nAnT-iCAGE protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MOI.12h.4
|
| Data processing |
The sequenced reads were processed using the MOIRAI pipeline. After filtering for ribosomal and low-quality reads, they were mapped to the mouse genome (mm9) using BWA version 0.5.9 (r16) to calculate gene expression.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include CPM values for each sample.
|
| |
|
| Submission date |
Dec 06, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Shiori Maeda |
| E-mail(s) |
shiori.maeda@riken.jp
|
| Organization name |
RIKEN
|
| Department |
Center for Integrative Medical Sciences
|
| Lab |
Laboratory for Cellular Function Conversion Technology
|
| Street address |
1-7-22 Suehiro-cho Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE249460 |
Transcriptome analysis of long non-coding RNAs in Mycobacterium avium complex-infected macrophages |
|
| Relations |
| BioSample |
SAMN38692513 |
| SRA |
SRX22797613 |
