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Status |
Public on Jan 28, 2022 |
Title |
H3K27ac_HiChIP_Ctrl_mOPC_rep2 |
Sample type |
SRA |
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|
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: Ctrl
|
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
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
replicate 2 P17103_1003 OPC_h3k27ac_hichip.hic Ctrl_5kb_EnhancerPredictions.bedpe Ctrl_5kb_EnhancerPredictionsFull.txt Ctrl_5kb_EnhancerPredictions.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.
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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 |
Solnavägen 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 |
SAMN17797048 |
SRA |
SRX10024542 |