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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2022 |
| Title |
scRNA_MEF_Ola_IFNb_6h_Rep1_merged |
| Sample type |
SRA |
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| Source name |
Mouse embryonic fibroblasts
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| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblasts
strain: 129/Ola
treatment: IFNb_6h
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| Treatment protocol |
All cells were treated with 500U/ml of self-made interferon beta (16.6U/µl) for 1 hour or 6 hours
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| Growth protocol |
Embryonic stem cells: Cultured on 0.1 % gelatinized tissue flasks in ESC media. Cells were incubated at 37 °C and 5 % CO2. Media was PowerStem ESPro1 (PAN-Biotech; P04-77510K) with self-made LIF (1:1000).
Mouse embryonic fibroblasts: Cells were incubated at 37 °C and 5 % CO2. Media was DMEM (Gibco, 11880-28), 10% FCS (PAN-Biotech; P30-3602), 1x L-Glutamine (PAN-Biotech, P04-80050), 1x PenStrep (PAN-Biotech, P06-07050).
Neural progenitor cells: ESCs were differentiated into NPCs based on the Bible-protocol Bibel et al. 2007. 4-5*10^6 cultured ESCs were split onto a T75 UltraLow-BindingPlates (Corning, 3814) in 15 ml StemPAN media (PAN-biotech, P08-50500). After 4 days 5µM retinoic acid (Sigma-Aldrich, R2625) was added. On day 8, cells were platted on plates coated with 1% Matrigel (Corning, 356230) in neuronal base medium (Gibco, 211103049), G5 supplements (Gibco, 17503012), NSC supplements (Gibco, 17502048). Experiments were performed five days after neuronal plating.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).
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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 |
scRNA-seq: Raw reads were applied to CellRanger (v1.3.1), a full automatic pipeline especially for scRNA-seq data done by the 10x Chromium.
scRNA-seq counttable: The default output folders with the counttable for downstream analysis.
supplementary file format and content: scRNA-seq: The folder contains the deault output of Cellranger. A list of detected barcodes in the sample. A List of identified genes in the sample as ENSEMBL ID and gene symbole. And a matix which is the counttable.
Genome_build: mm10
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| Submission date |
Feb 01, 2022 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Markus Muckenhuber |
| E-mail(s) |
m.muckenhuber@dkfz.de
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| Organization name |
DKFZ
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| Lab |
AG Rippe
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE160764 |
Epigenetic signals that direct cell type specific interferon beta response in mouse cells |
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| Relations |
| BioSample |
SAMN25554424 |
| SRA |
SRX14005097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5852365_scRNA_MEF_Ola_6h_Rep1_filtered_gene_bc_matrices.tar.gz |
96.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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