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| Status |
Public on Oct 01, 2024 |
| Title |
NC059 aCM+M1 biol rep 1 |
| Sample type |
SRA |
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| Source name |
Cell line 2 (NC-059)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Cell line 2 (NC-059)
cell type: hiPSC-derived atrial cardiomyocyte
genotype: WT
treatment: M1 coculture
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| Treatment protocol |
For M1 coculture and M1 conditioned medium: Maturation of monocytes towards M1 macrophages was performed by supplementing culture medium with 20 ng/mL GM-CSF (Gibco) for 6 days, with medium being refreshed at d3. Matured M1 macrophages were activated by adding 100 ng/mL IFN-γ (Peprotech) and 50 ng/mL LPS (InvivoGen) at d6 for 20h, followed by a change of medium with 100 ng/mL LPS added for 4h. For Hydrocortisone Treatment: Hydrocortisone 10 µM was added to cells. Cocultures were seeded and cultured as previously described and hydrocortisone added during medium changes at d6, d6+20h, d7 and d8 after seeding. For conditioned medium samples: For conditioned medium samples, 125 ul supernatant from M1 monocultures (24 well plate, 500,000 cells/well in 0.5 mL PCM) was added to appropriate samples.
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| Growth protocol |
Cells were cultured in PCM (Ncardia) at 37C and 5% CO2 until 8 days after seeding
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| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin RNA, Mini kit for RNA purification (According to manufacturer protocol), (Machery-Nagel)
Performed by Single Cell Discoveries (Netherlands) 1. Pre-quality checks to measure RNA concentration and RNA quality 2. Performing RT to generate cDNA 3. Pooling of all samples (barcodes are now integrated within the cDNA molecules) 4. Amplification of the material through an IVT reaction (linear amplification), which generates amplified RNA 5. QC: bioanalyzer of the amplified RNA 6. Library preparation to generate a sequenceable cDNA library (aRNA) 7. QC: bioanalyzer of the final cDNA library
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
#13 aCM+M1 s1 N
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| Data processing |
Performed by Singe Cell Discoveries (Netherlands)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
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| Submission date |
Jul 07, 2023 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Thomas Hutschalik |
| Organization name |
Ncardia Services B.V.
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| Street address |
Galileiweg 8
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| City |
Leiden |
| ZIP/Postal code |
2333 BD |
| Country |
Netherlands |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE236870 |
M1 Macrophages cause cardiac arrhythmia in an in vitro hiPSC coculture model of inflammation-induced atrial fibrillation |
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| Relations |
| BioSample |
SAMN36359579 |
| SRA |
SRX20942166 |
| 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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