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Sample GSM3509510 Query DataSets for GSM3509510
Status Public on Jul 01, 2020
Title mESC_ATAC-seq_SL_rep3
Sample type SRA
Source name mouse embryonic stem cells
Organism Mus musculus
Characteristics cell type: mouse embryonic stem cells
culture condition: cultured with serum/LIF (SL)
Growth protocol ESCs in SL medium were cultured in DMEM/high glucose containing 15% FBS, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, and 1,000 U/ml LIF on mitomycin-C treated mouse embryonic fibroblasts (MEFs), and they were split onto 0.2% gelatin pre-coated plates prior to the experiment. ESCs in 2iL medium were cultured in a 1:1 mix of DMEM/F12 and Neurobasal medium, with N2 and B27 supplements, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, 1,000 U/ml LIF, 3 μM, and 1 μM PD0325901 on 0.2% gelatin pre-coated plates.
Extracted molecule genomic DNA
Extraction protocol A total of 50,000 cells were washed once with cold PBS and re-suspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA-630). The suspension were then centrifuged at 500 g for 10 min at 4°C, following by addition of 50 μl transposition reaction mix of TruePrep DNA Library Prep Kit. Then, samples were incubated at 37°C for 30 mins. Transposition reactions were cleaned up using a MinElute PCR Purification Kit. ATAC-seq libraries were subjected to 5 cycles for pre-amplification and then amplified by PCR for an appropriate number of cycles. The amplified libraries were purified with a QIAquick PCR Purification Kit. Libraries were sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) according to the manufacturer’s instructions.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Illumina bcl2fastq2.17 software was used for base-calling.
Adapter and transposon sequence were trimmed using cutadapt(v 1.1.8).
Data were first aligned to the mm10 mouse genome assembly using Bowtie2 (v2.2.5) with the settings ‘--very-sensitive’. Low quality mapped reads were removed using Samtools with the settings ‘-q 30’. Duplicated reads were collapsed using Picard.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage script of deepTools with the options “ --binSize 10 --normalizeUsingRPKM”.
Submission date Dec 12, 2018
Last update date Jul 02, 2020
Contact name Yiwei Lai
Organization name Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences
Department South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS
Lab Miguel
Street address 190 Kai Yuan Avenue, Science Park
City Guangzhou
State/province Guangdong
ZIP/Postal code 510530
Country China
Platform ID GPL19057
Series (2)
GSE123690 β-catenin safeguards the ground state of pluripotency by strengthening the robustness of the transcriptional apparatus [ATAC-seq]
GSE123692 β-catenin safeguards the ground state of pluripotency by strengthening the robustness of the transcriptional apparatus
BioSample SAMN10585014
SRA SRX5126501

Supplementary file Size Download File type/resource 402.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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