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Sample GSM3963698 Query DataSets for GSM3963698
Status Public on Jul 24, 2019
Title Macrophages in a co-culture system with BMSCs, MSR1 WT_3
Sample type SRA
Source name Macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: BMM derived macrophages
genotype: MSR1 WT
Treatment protocol Further, macrophages from MSR1 KO or WT mice were co-cultured with BMSCs via a transwell system for 48h.
Growth protocol To obtain primary bone marrow-derived macrophages, bone marrow cells first underwent lysis of red blood cells and were then resuspended in complete RPMI-1640 medium consisting of 25 ng/ml macrophage colony-stimulating factor (M-CSF) and cultured for 7 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina Hiseq X Ten according the manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Data processing fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Genome_build: gencode v27
Supplementary_files_format_and_content: comma-delimited text file including RPKM values and counts for each Sample
Submission date Jul 23, 2019
Last update date Jul 27, 2019
Contact name Shujie Zhao
Organization name Department of Orthopedic, The First Affiliated Hospital of Nanjing Medical University
Street address longmian street
City Nanjing
ZIP/Postal code 210000
Country China
Platform ID GPL21273
Series (1)
GSE134693 The effect of MSR1 knockout in macrophages in a co-culture system with BMSCs
BioSample SAMN12341708
SRA SRX6490848

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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