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Sample GSM3963697 Query DataSets for GSM3963697
Status Public on Jul 24, 2019
Title Macrophages in a co-culture system with BMSCs, MSR1 WT_2
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
E-mail(s) nydshenyifei@126.com
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
Relations
BioSample SAMN12341709
SRA SRX6490847

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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