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Sample GSM5065199 Query DataSets for GSM5065199
Status Public on Jan 28, 2022
Title H3K27ac_HiChIP_IFN_mOPC_rep1
Sample type SRA
 
Source name Mouse brain
Organism Mus musculus
Characteristics strain: C57BL/6j
genotype: Sox10-Cre/RCE
chip antibody: Abcam Ab177178
tn5: In-house Tn5
cell type: cultured primary mOPCs
treatment: IFN
Treatment protocol 24hours after passaging the cells, cells were incubated in Control medium (OPC proliferation medium) or IFNg medium (OPC proliferation medium + 100ng/mL IFNg)
Growth protocol Cells were cultured in OPC proliferation medium (DMEM/Glutamax, 1xN2 supplement, 1x Penicilin-streptomycin, 1x NeuroBrew, 20ng/mL bFGF, 20ng/mL mPDGF-AA)
Extracted molecule genomic DNA
Extraction protocol Cells were harvested using TrypLE and fixed with 1% formaldehyde prior to processing for HiChIP
Libraries were prepared as specified in Mumbach et.al. (2016) and with 0.75uL Tn5 enzyme.
Samples were sequenced on a single-lane of an SP flowcell on the NovaSeq6000 with the 2x50bp read setup
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description replicate 1
P17103_1002
OPC_h3k27ac_hichip.hic
IFNg_5kb_EnhancerPredictions.txt
IFNg_5kb_EnhancerPredictions.bedpe
IFNg_5kb_EnhancerPredictionsFull.txt
Data processing Library strategy: HiChIP
Fastq files were aligned to the mm10 genome and filtered for duplicate reads using the HiC-Pro pipeline.
allValidPairs files from the HiC-Pro pipeline for each replicate were merged together
hicpro2juicebox.sh from HiC-Pro was used on the merged allValidPairs file to generate the .hic file in the Ctrl OPCs. Enhancer promoter interactions were called using ABC model with a 5Kb window size.
Genome_build: mm10
Supplementary_files_format_and_content: Juicebox compatible .hic file, contains contact matrix for Ctrl OPCs. Enhancer promoters interactions called with ABC model for Ctrl OPC and IFNg OPCs in bed format , bedpe. All the enhancer promoter interactions predicted with the ABC model in a tab separated file complementary of the bedpe files are provided.
 
Submission date Feb 04, 2021
Last update date Jan 28, 2022
Contact name Eneritz Agirre
Organization name Karolinska Institutet
Department MBB
Lab Castelo-Branco, Molecular Neurobiology
Street address Solnav├Ągen 9
City Stockholm
ZIP/Postal code 17165
Country Sweden
 
Platform ID GPL24247
Series (2)
GSE166177 A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [HiChIP]
GSE166179 A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis
Relations
BioSample SAMN17797050
SRA SRX10024541

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

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