|
| Status |
Public on Jul 01, 2024 |
| Title |
Active tuberculosis infection replicate 4 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood NK cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood NK cells
treatment: No treatment
disease state: Active tuberculosis infection
age: 18
biomaterial provider: Cui Hua Liu's lab
Sex: Male
ethnicity: Colored
bmi: 21.61
smoking status: Never
bcg scar: Present
previous diagnosis_of_tb: No
igra: Positive
pulmonary cavitation: No
mtb culture: Yes
drug resistant_tb: No
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from purified NK cells using RNA Isolation Kit (Dongsheng, R1061) according to the manufacturer’s instructions.
RNA-Sequencing was conducted using the Illumina HiSeq X Ten platform (Novogene Bioinformatics Technology Co., Ltd.) with paired-end 150-bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
TB-rep4
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
|
| |
|
| Submission date |
Jan 02, 2023 |
| Last update date |
Jul 01, 2024 |
| Contact name |
lu z |
| E-mail(s) |
[email protected]
|
| Organization name |
institution of microbology
|
| Lab |
liuch
|
| Street address |
beijing
|
| City |
beijing |
| State/province |
- 选择 - |
| ZIP/Postal code |
10010 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE222001 |
Transcriptional profiling of NK cells from tuberculosis patients |
|
| Relations |
| BioSample |
SAMN32406382 |
| SRA |
SRX18861718 |
