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Status |
Public on Jan 31, 2017 |
Title |
s04-suscep-infect |
Sample type |
SRA |
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Source name |
monocyte-derived dendritic cells
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Organism |
Homo sapiens |
Characteristics |
cell type: monocyte-derived dendritic cells individual: s04 status: susceptible treatment: infected gender: male
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Treatment protocol |
We infected the DCs with Mycobacterium tuberculosis (MTB) H37Rv at a multiplicity of infection of 1-to-1 for 18 hours.
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Growth protocol |
We isolated mononuclear cells from the whole blood samples using Ficoll-Paque centrifugation, extracted monocytes via CD14 positive selection, and differentiated the monocytes into dendritic cells (DCs) by culturing them for 5 days in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools).
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Extracted molecule |
polyA RNA |
Extraction protocol |
We extracted RNA using the Qiagen miRNeasy Kit. We prepared sequencing libraries using the Illumina TruSeq Kit.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
We mapped reads to human genome hg38 (GRCh38) using Subread (v1.5.0-p2) and discarded non-uniquely mapping reads (flag -u). We downloaded the exon coordinates of 19,800 Ensembl protein-coding genes (Ensembl 83, Dec 2015, GRCh38.p5) using the R(3.2.1)/Bioconductor(3.2) package biomaRt (2.26.1) and assigned mapped reads to these genes using featureCounts (v1.5.0-p2). We filtered genes based on their expression level by removing all genes with a transformed median log2 counts per million (cpm) of less than zero. This step resulted in a set of 11,336 genes for downstream analysis. Genome_build: hg38 Supplementary_files_format_and_content: Supplementary_Data_S1.tds (tab-delimited) contains information on the 50 samples. Most variables describe the batch processing steps. “id” is a unique identifier for each sample, “individual” is the individual identifier (“s” = susceptible, “r” = resistant), “status” is the susceptibility status, “treatment” is if the sample was infected or non-infected, “infection” is the date of the infection experiment (12 total), “arrival” is the identifier for the arrival batch (4 total), “extraction” is the batch for RNA extraction (5 total), “master_mix” is the batch for library preparation (3 total), “rin” is the RNA Integrity Number from the Agilent Bioanalyzer, and “outlier” is a Boolean variable indicating if the sample was identified as an outlier and removed from the analysis. Supplementary_files_format_and_content: Supplementary_Data_S2.tds (tab-delimited) contains the gene expression counts for the 11,336 genes after filtering lowly expressed genes for all 50 samples. Each row is a gene labeled with its Ensembl gene ID. Each column is a sample. Each sample is labeled according to the pattern “x##-status-treatment”, where x is “r” for resistant or “s” for susceptible, ## is the ID number, status is “resist” for resistant or “suscep” for susceptible, and treatment is “noninf” for non-infected or “infect” for infected.
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Submission date |
Jan 26, 2017 |
Last update date |
May 15, 2019 |
Contact name |
John D Blischak |
Organization name |
University of Chicago
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Department |
Human Genetics
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Lab |
Gilad
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Street address |
920 E. 58th Street, CLSC 317
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City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60615 |
Country |
USA |
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Platform ID |
GPL20301 |
Series (1) |
GSE94116 |
Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells |
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Relations |
BioSample |
SAMN06274468 |
SRA |
SRX2520715 |
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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