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Series GSE108393 Query DataSets for GSE108393
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
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.
Overall design NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to early secreted antigenic target 6-KDa (ESAT6) stimulation in phagosome.
Contributor(s) Chen M, Li F
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Submission date Dec 21, 2017
Last update date Dec 21, 2020
Contact name Fake Li
Phone 8613677631560
Organization name Daping Hospital
Department Clinical Laboratory Medicine
Lab Gezhi Lab
Street address Changjiangzhilu 10 Yuzhong District
City Chongqing
State/province Chongqing
ZIP/Postal code 400042
Country China
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (4)
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
BioProject PRJNA427122
SRA SRP127327

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Supplementary file Size Download File type/resource
GSE108393_TMM_normalized_reads_count_per_million-nESAT6.xlsx.gz 1.3 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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