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| Status |
Public on Dec 21, 2020 |
| Title |
RNA-seq identifies a distinct response in macrophages stimulated from phagosome with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis |
| Organism |
Homo sapiens |
| Experiment type |
Expression 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, which were stimulated from phagosome with early secreted antigenic target 6-KDa (ESAT6)
Methods: First we fabricated a nanocapsule enclosing ESAT6 (nESAT6) and a nanocapsule enclosing BSA (nBSA) as control. mRNA profiles of THP-1 macrophages treated with nESAT6 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), and 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 23 million sequence reads per sample to the human genome (GRCh38/hg38) and identified 25,343 transcripts.
Conclusions: Our study represents the first detailed analysis of transcriptomes for macrophages response to ESAT6 stimulation in phagosome, generated by RNA-seq technology.
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| Overall design |
NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to early secreted antigenic target 6-KDa (ESAT6) stimulation in phagosome.
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| Contributor(s) |
Chen M, Li F |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 21, 2017 |
| Last update date |
Dec 21, 2020 |
| 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
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| 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 (4)
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| GSM2897329 |
THP-1 macrophages stimulated with nBSA for 4 hours |
| GSM2897330 |
THP-1 macrophages stimulated with nBSA for 24 hours |
| GSM2897331 |
THP-1 macrophages stimulated with nESAT6 for 4 hours |
| GSM2897332 |
THP-1 macrophages stimulated with nESAT6 for 24 hours |
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| Relations |
| BioProject |
PRJNA427122 |
| SRA |
SRP127327 |
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