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| Status |
Public on Jan 04, 2021 |
| Title |
RNA-seq identifies a distinct response in macrophages infected with Mycobacterium tuberculosis for a serial time points. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study are to obtain the NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to Mycobacterium tuberculosis (H37Rv and H37Ra)
Methods: mRNA and long noncoding RNA profiles of THP-1 macrophages infected with H37Rv and H37Ra for 1, 4, 12, 24, 48 hours were generated by deep sequencing, using Illumina Hiseq3000. The sequence reads that passed quality filters were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0). Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15), for lncRNA analysis, reads were mapped to lncRNA transcript set from LNCipedia.org. The sequence reads were normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package edgeR. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the human genome (GRCh38/hg38) and identified 25,343 mRNA and 47877 long non-coding RNA transcripts.
Conclusions: Our study represents the detailed analysis of transcriptomes for THP-1 macrophages response to H37Rv and H37Ra, generated by RNA-seq technology.
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| Overall design |
NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to Mycobacterium tuberculosis H37Rv and H37Ra.
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| Contributor(s) |
Li F, Luo J, Xu H, Chen M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jan 04, 2018 |
| Last update date |
Jan 04, 2021 |
| Contact name |
Fake Li |
| E-mail(s) |
cqlfk@hotmail.com
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| Phone |
8613677631560
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| Organization name |
Daping Hospital
|
| Department |
Clinical Laboratory Medicine
|
| Lab |
Gezhi Lab
|
| Street address |
Changjiangzhilu 10 Yuzhong District
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| City |
Chongqing |
| State/province |
Chongqing |
| ZIP/Postal code |
400042 |
| Country |
China |
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| Platforms (1) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA428439 |
| SRA |
SRP128019 |
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