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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.
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
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
BioSample SAMN30078749
SRA SRX16749826

Supplementary file Size Download File type/resource 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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