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Sample GSM6423425 Query DataSets for GSM6423425
Status Public on Jun 20, 2023
Title hMeDIP-seq in WT
Sample type SRA
 
Source name V6.5
Organism Mus musculus
Characteristics cell line: V6.5
cell type: mouse embryonic stem cells
treatment: non
chip antibody: Active motif 39769
Growth protocol Feeder-free Mouse V6.5 embryonic stem cells were cultured on 0.1% gelatin-coated plates. mESCs were cultured in N2B27 medium (50% DMEM/F12 and 50%Neurobasal medium, 1x N2 supplement, 1x B27 supplement ,1x Penicillin-Streptomycin, 0.1 mM mercaptoethanol, 2 mM L-glutamine) supplemented with Mek inhibitor (PD0325901, 2.5 M),Gsk3 inhibitor (CHIR99021, 7.5 M) and 5 units of LIF, at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.
Extracted molecule genomic DNA
Extraction protocol cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature.5 μg of genomic DNA was sheared into 200-500 bp using Bioruptor (Diagenode) for 13 cycles with 30s on, 60s off. Sonicated DNA was immunoprecipitated with 5 μg of 5hmc antibody for 2 hrs at 4  °C, then Protein A/G beads was added into the DNA-antibody mixture and samples were incubated for another 2 hrs at 4  °C. DNA was purified from the elutant using FastPure Gel DNA Extraction Mini Kit (Vazyme).
The sequencing library was generated from purified ssDNA (10 ng) with Scale ssDNA-seq Lib Prep Kit (Abclonal) and amplified by PCR. Libraries with different indexes were pooled and sequenced using Illumina HiSeq sequencing systems.
hMeDIP-seq
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina NovaSeq 6000
 
Data processing For quantification of repetitive genomic regions, allowed multiple-mapping reads using Bowtie2 parameter ‘–fast -k 1’.
Assembly: mm9
 
Submission date Aug 01, 2022
Last update date Jun 20, 2023
Contact name Xiaoxu Liu
E-mail(s) liuxiaoxu1010@126.com
Organization name Southeast University
Department Institute of Life Sciences
Lab the Key Laboratory of Developmental Genes and Human Disease
Street address 2 Sipailou
City Nanjing
State/province Jiangsu
ZIP/Postal code 210018
Country China
 
Platform ID GPL24247
Series (2)
GSE207397 ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ChIP-Seq]
GSE208227 ELL3 promotes stem cell native to primed transition through LINE-based enhancers
Relations
BioSample SAMN30078749
SRA SRX16749826

Supplementary file Size Download File type/resource
GSM6423425_hMeDIP-seq_of_5hmc_in_WT_2iL.bw 130.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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