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Sample GSM7809958 Query DataSets for GSM7809958
Status Public on Aug 09, 2024
Title P28 cortical neurons Nanopore Sequencing rep2
Sample type SRA
 
Source name cortex
Organism Mus musculus
Characteristics tissue: cortex
cell type: neuron
genotype: WT
developmental stage: P28
Extracted molecule genomic DNA
Extraction protocol High molecular weight (HMW) DNA was extracted from isolated cells using the Monarch HMW DNA extraction kit (New England Biolabs, #T3050L) following the manufacturer’s instructions.
The HMW DNA was sheared to 20kb with g-TUBE (Covaris #520079). Library preparation was following Nanopore protocols to attach sequencing adapters to the DNA ends with Ligation Sequencing Kit (Oxford Nanopore Technologies, #SQK-LSK110). One flow cell was applied for each library to ensure an optimal sequencing depth of around 20x coverage at each cytosine and sequenced on PromethION (Steger Hall sequencing core, Virginia Tech).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model PromethION
 
Description Methylation_5mC_sites_cov9.bed.gz
Methylation_5hmC_sites_cov9.bed.gz
DMS_Astrocyte_Neuron_5mC_cov9.bed.gz
DMS_Neuron_Microglia_5mC_cov9.bed.gz
DMS_Astrocyte_Neuron_5hmC_cov9.bed.gz
DMS_Neuron_Microglia_5hmC_cov9.bed.gz
Data processing The raw signal stored in fast5 files were converted to nucleotide sequence, which were mapped to the mouse reference genome mm10 with the tool megalodon (v 2.4.2). Quality control was performed using the tool, pycoQC (v2.5.2) with the sequencing summary file generated by Megalodon.
Methylated CpG sites were distinguished based on the electronic signal difference and mapping result with the model provided by Remora (v0.1.2). The final output provides the position and quantitative methylation level of each cytosine site for both 5mc and 5hmc modification.
Only CpG sites with average coverage greater than 3 and identified in at least two libraries were used for the following analysis. Methylated sites were defined as CpG sites with methylation levels over 10%. DMSs and DMRs among neurons, astrocytes and microglia were identified with the R package DSS (v2.44.0) with smoothing = T setting.
Only sites with methylation level difference greater than 10% and FDR less than 0.01 were considered as DMSs.
Assembly: mm10
 
Submission date Sep 28, 2023
Last update date Aug 09, 2024
Contact name Michelle Lynne Olsen
E-mail(s) molsen1@vt.edu
Organization name Virginia Tech
Department School of Neuroscience
Lab Olsen Lab
Street address 970 Washington Street SW
City Blacksburg
State/province VA
ZIP/Postal code 24060
Country USA
 
Platform ID GPL26624
Series (2)
GSE244251 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [Nanopore]
GSE244256 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain
Relations
BioSample SAMN37413695
SRA SRX21796929

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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