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Sample GSM5852364 Query DataSets for GSM5852364
Status Public on Dec 31, 2022
Title scRNA_MEF_Ola_IFNb_1h_Rep1_merged
Sample type SRA
 
Source name Mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: Mouse embryonic fibroblasts
strain: 129/Ola
treatment: IFNb_1h
Treatment protocol All cells were treated with 500U/ml of self-made interferon beta (16.6U/µl) for 1 hour or 6 hours
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Feb 01, 2022
Last update date Dec 31, 2022
Contact name Markus Muckenhuber
E-mail(s) m.muckenhuber@dkfz.de
Organization name DKFZ
Lab AG Rippe
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL24247
Series (1)
GSE160764 Epigenetic signals that direct cell type specific interferon beta response in mouse cells
Relations
BioSample SAMN25554422
SRA SRX14005096

Supplementary file Size Download File type/resource
GSM5852364_scRNA_MEF_Ola_1h_Rep1_filtered_gene_bc_matrices.tar.gz 98.3 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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