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| Status |
Public on Jul 01, 2020 |
| Title |
mESC_ATAC-seq_SL_rep1 |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
culture condition: cultured with serum/LIF (SL)
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| 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.
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| 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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”.
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| Submission date |
Dec 12, 2018 |
| Last update date |
Jul 02, 2020 |
| Contact name |
Yiwei Lai |
| E-mail(s) |
[email protected]
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| Organization name |
Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences
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| Department |
South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS
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| Lab |
Miguel
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| Street address |
190 Kai Yuan Avenue, Science Park
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN10585017 |
| SRA |
SRX5126499 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3509508_mESC_ATAC-seq_SL_rep1.bw |
311.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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