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Status |
Public on Nov 18, 2019 |
Title |
BM-WT-monocytes |
Sample type |
SRA |
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Source name |
monocytes isolated from the bone marrow following EAE induction
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6J tissue: Bone marrow cell type: Monocytes
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Treatment protocol |
Experimental autoimmune encephalomyelitis (EAE) was induced in mice on a C57BL/6J background by subcutaneously injection of myelin oligodendrocyte glycoprotein peptide emulsified in complete Freund’s adjuvant. Pertussis toxin (250 ng) was injected intraperitoneally at 2- and 24-hours following the injection of emulsion.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA from the purified monocytes and monocyte-derived cells was isolated using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) with 300 ng of total RNA and 11 cycles of PCR according to manufacturer’s recommendation. The libraries were quantified using Qubit Fluorometer, and the quality of the libraries was determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA, USA).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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Data processing |
Transcript abundance estimated by Salmon 0.14.1 (PMID: 28263959) based on whole transcripts annotation by gencode vM22 (PMID: 22955987). Genome_build: mm10 Supplementary_files_format_and_content: Txt file, output from salmon columns from left to right represent "Name", "Length", "EffectiveLength", "TPM" (transcripts per million pair-end reads), and "NumReads".
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Submission date |
Sep 20, 2019 |
Last update date |
Nov 19, 2019 |
Contact name |
Gangqing Hu |
E-mail(s) |
michael.hu@hsc.wvu.edu
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Organization name |
West Virginia University
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Department |
MicroBiology, Immunology, and Cell Biology
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Lab |
2072A, HSC North, Floor 2
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Street address |
64 Medical Center Drive
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City |
Morgantown |
State/province |
West Virginia |
ZIP/Postal code |
26506-9177 |
Country |
USA |
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Platform ID |
GPL18480 |
Series (1) |
GSE137801 |
Monocytes and Monocyte-derived Antigen-presenting Cells have Distinct Gene Signatures in Experimental Model of Multiple Sclerosis |
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Relations |
BioSample |
SAMN12799184 |
SRA |
SRX6881600 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4088762_BM-WT-monocytes_gencode_vM22_quant_genes_sf_salmon.txt.gz |
712.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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