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Series GSE108731 Query DataSets for GSE108731
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
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 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.
Overall design NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to Mycobacterium tuberculosis H37Rv and H37Ra.
Contributor(s) Li F, Luo J, Xu H, Chen M
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Submission date Jan 04, 2018
Last update date Jan 04, 2021
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 (16)
GSM2912649 THP-1 macrophages uninfected_0h
GSM2912650 THP-1 macrophages uninfected_1h
GSM2912651 THP-1 macrophages uninfected_4h
BioProject PRJNA428439
SRA SRP128019

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Supplementary file Size Download File type/resource
GSE108731_TMM_normalized_reads_count_per_million-MTB-mRNA.xlsx.gz 3.6 Mb (ftp)(http) XLSX
GSE108731_TMM_normalized_reads_count_per_million_MTB-lncRNA.xlsx.gz 4.0 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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