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Series GSE107387 Query DataSets for GSE107387
Status Public on Mar 10, 2019
Title RNA-seq identifies a distinct response in macrophages stimulated 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 response to early secreted antigenic target 6-KDa (ESAT6) from Mycobacterium tuberculosis
Methods: mRNA profiles of THP-1 macrophages treated with ESAT6 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, 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) from Mycobacterium tuberculosis.
Contributor(s) Chen M, Li F
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Submission date Nov 27, 2017
Last update date May 15, 2019
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 (3)
GSM2865802 THP-1 macrophages unstimulated
GSM2865803 ESAT6_4h
GSM2865804 ESAT6_24h
BioProject PRJNA419953
SRA SRP125701

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE107387_TMM_normalized_reads_count_per_million-ESAT6.txt.gz 633.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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