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Sample GSM4088762 Query DataSets for GSM4088762
Status Public on Nov 18, 2019
Title BM-WT-monocytes
Sample type SRA
 
Source name monocytes isolated from the bone marrow following EAE induction
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: Bone marrow
cell type: Monocytes
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
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".
 
Submission date Sep 20, 2019
Last update date Nov 19, 2019
Contact name Gangqing Hu
E-mail(s) michael.hu@hsc.wvu.edu
Organization name West Virginia University
Department MicroBiology, Immunology, and Cell Biology
Lab 2072A, HSC North, Floor 2
Street address 64 Medical Center Drive
City Morgantown
State/province West Virginia
ZIP/Postal code 26506-9177
Country USA
 
Platform ID GPL18480
Series (1)
GSE137801 Monocytes and Monocyte-derived Antigen-presenting Cells have Distinct Gene Signatures in Experimental Model of Multiple Sclerosis
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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