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| Status |
Public on Jan 04, 2021 |
| Title |
H37Ra_4h |
| Sample type |
SRA |
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| Source name |
THP-1 macrophages
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| Organism |
Homo sapiens |
| Characteristics |
cell type: THP-1 macrophages
agent: H37Ra
time point: 4h
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| Treatment protocol |
THP-1 macrophages were uninfected or infected with Mycobacteria tuberculosis H37Rv and H37Ra at MOI=3 for 1 h, 4 h, 12 h, 24 h or 48 h. Cells were placed in a humidified, 37℃ 5% CO2 incubator.
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| Growth protocol |
Human monocyte cell line THP-1 cells were cultured in RPMI 1640 basic medium (Gibco, life technologies, USA) supplemented with 2 mM L-glutamine, Penicillin (100 U/ml)-Streptomycin (100 µg/ml) Solution and 10% fetal bovine serum (FBS) (Catalog No. 04-121-1A, Biological Industries, Israel) at cultural density of 5 × 105 - 1 × 106/ml.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA were isolated with RNeasy mini kit (Qiagen, Germany) according to the manufacturer's instructions
Both rRNA and mitochondrial RNA was removed with Ribo-Zero Gold Removal Magnetic Kit for human/mouse/rat (Epicentre, now Illumina) according to the manufacturer’s instructions. The libraries were prepared with KAPA RNA-Seq Kit for Illumina (Kapa biosystems, USA) following the manufacturer's procedure. The RNA was fragmented to the desired size (about 300 bp) by heating in the presence of Mg++. The 1st strand cDNA was synthesized with random primers. The 2nd strand cDNA synthesis converted cDNA:RNA hybrid to double strand cDNA (dscDNA), while marking the 2nd strand with dUTP. Then dAMP was added to 3’-end of dscDNA fragments. Following by ligation of 3’-dTMP adapters (10 nM) to 3’-dAMP library fragments, and PCR amplification (14 cycles) of the adapter-ligated library DNA. The dUTP-marked strand was not amplified. Library fragment size distribution was confirmed by electrophoresis and library concentration was determined with Qubit 2.0 Fluorometric Quantitation (Thermo Fisher Scientific, USA). These libraries were sequenced using the Illumina Hiseq 3000 Sequencer (50 cycles, single read lane).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Ra4H
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| Data processing |
Quality control analysis of the raw sequence files was conducted with FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The quality-checked reads for each condition 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.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample ...
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| 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
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| Department |
Clinical Laboratory Medicine
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| Lab |
Gezhi Lab
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| 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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| Platform ID |
GPL21290 |
| Series (1) |
| GSE108731 |
RNA-seq identifies a distinct response in macrophages infected with Mycobacterium tuberculosis for a serial time points. |
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| Relations |
| BioSample |
SAMN08290480 |
| SRA |
SRX3530806 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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