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Sample GSM5852376 Query DataSets for GSM5852376
Status Public on Dec 31, 2022
Title ChIP_MEF_Ola_H3K9ac_IFNb_0h_Rep1
Sample type SRA
 
Source name Mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: Mouse embryonic fibroblasts
strain: 129/Ola
treatment: IFNb_0h
chip antibody: 39137; Active Motif; #lot 16111002
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 genomic DNA
Extraction protocol ChIP-seq for histone marks in MEFs: Cells were crosslinked by 1 % Formaldehyde for 10 min at room temperature and stopped with 125 mM Glycine for 5 min. Samples of around 40 million cells were treated with 40 U of MNase for 15 min at 37 °C. The samples were shared for 15 min (Burst 200; Cycle 20%; Intensity 8). Replicate 1 was shared for 30 min and no MNase treatment was performed. 4µg of antibody was used per sample and incubated for 2 hours at 4 °C. Protein G-beads were added over night. Multiple low and high salt washes were performed and the samples were eluted. Samples were reverse crosslinked and stored at -20°C.
ChIP-seq for histone marks in MEFs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing ChIP bed files: Raw reads were mapped with Bowtie (v1.2.2). The mapped reads were sorted, duplicates and reads in blacklisted regions removed with bedtools (v2.27.1).
ChIP Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control. For histon marks H3 signal was the control. For STAT ChIPs IgG_Rb_CST.
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 GPL13112
Series (1)
GSE160764 Epigenetic signals that direct cell type specific interferon beta response in mouse cells
Relations
BioSample SAMN25554436
SRA SRX14005110

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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