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| Status |
Public on Aug 02, 2024 |
| Title |
BMDMs, WT1_0h |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
strain: C57Bl6/J
cell type: bone marrow-derived macrophages
genotype: wt
treatment: untreated
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| Treatment protocol |
Cells were stimulated with 100 ng/ml LPS for 0, 4 and 18h
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| Growth protocol |
Bone marrow cells were isolated from the femurs and tibias of male WT and Nur77-KO mice aged 6-12 weeks. The cells were differentiated into macrophages by culturing them in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 15% L929-conditioned medium, 1 mM sodium pyruvate, 1x MEM Non-Essential Amino Acids Solution, and 1x MEM Vitamin Solution for a period of 7 days. After the differentiation process, the cells were lifted, counted, and re-seeded at a density of 1 × 10^6 cells per ml.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts for each sample
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| Submission date |
Jan 16, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
Claudia van Tiel |
| E-mail(s) |
c.m.vantiel@amsterdamumc.nl
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| Organization name |
Amsterdam UMC
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| Department |
Medical Biochemistry
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| Street address |
Meibergdreef 15
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| City |
Amsterdam |
| ZIP/Postal code |
1105AZ |
| Country |
Netherlands |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE253423 |
Nuclear receptor Nur77 regulates immunomechanics of macrophages |
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| Relations |
| BioSample |
SAMN39463765 |
| SRA |
SRX23254159 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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