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| Status |
Public on Jul 24, 2019 |
| Title |
Macrophages in a co-culture system with BMSCs, MSR1 WT_1 |
| Sample type |
SRA |
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| Source name |
Macrophages
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: BMM derived macrophages
genotype: MSR1 WT
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| Treatment protocol |
Further, macrophages from MSR1 KO or WT mice were co-cultured with BMSCs via a transwell system for 48h.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| 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
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| Submission date |
Jul 23, 2019 |
| Last update date |
Jul 27, 2019 |
| Contact name |
Shujie Zhao |
| E-mail(s) |
nydshenyifei@126.com
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| Organization name |
Department of Orthopedic, The First Affiliated Hospital of Nanjing Medical University
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| Street address |
longmian street
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| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE134693 |
The effect of MSR1 knockout in macrophages in a co-culture system with BMSCs |
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| Relations |
| BioSample |
SAMN12341710 |
| SRA |
SRX6490846 |
| 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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