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| Status |
Public on Jun 22, 2023 |
| Title |
MEF Hdac7SA.Mef2d (ATAC-seq) rep1 |
| Sample type |
SRA |
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| Source name |
OG2 MEFs
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| Organism |
Mus musculus |
| Characteristics |
cell line: OG2 MEFs
cell type: MEF
genotype: Hdac7SA Mef2d immortalized
treatment: None
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| Treatment protocol |
MEFs were treated with the inhibitors PD0325901 and TSA for two days.
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| Growth protocol |
MEFs were derived from E13.5 embryos from wildtype ICR genetic background. MEF cells were cultured in DMEM high-glucose media containing 10% FBS (GIBCO), 1 × GlutaMAX (GIBCO), and 1x nonessential amino acids (GIBCO), 0.5x Penicillin/Streptomycin (Hyclone). We generated immortalized MEF cell lines and used the oncogenic genes: P53DD, PMM2-SV40T, PMM2-Hdac7SA, PMM2-Mef2d, Bcl2, PMM2-Myc, Ras, PMM2-E1A.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The nuclei were centrifuged for 10 min at 500 × g at 4 °C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase (Vazyme) and 22.5 μl nuclease-free water). Samples were PCR amplified and purified using a MinElute kit (Qiagen). After selecting an appropriate PCR cycle number (See (Buenrostro et al., 2013)) samples were sequenced on an Illumina sequencer.
ATAC-seq library was generated using the Tn5 enzyme from the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501-02) as previously described (Buenrostro et al., 2013). Briefly, a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The nuclei were centrifuged for 10 min at 500 × g at 4 °C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase (Vazyme) and 22.5 μl nuclease-free water). Samples were PCR amplified and purified using a MinElute kit (Qiagen).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Mm_atac_mef_hm.bed.gz
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| Data processing |
Reads were aligned to the mm10 mouse genome with bowtie2 (v2.4.5) (Langmead and Salzberg, 2012)
Peaks were called with MACS2 (v2.2.7.1) (Zhang et al., 2008)
redefine_peaks function, was used to recover low-scoring peaks by sharing peak information across samples (Ma et al., 2021)
All other analysis was performed using glbase3 (Hutchins et al., 2014).
Assembly: mm10
Supplementary files format and content: peak BED files
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| Submission date |
Sep 12, 2022 |
| Last update date |
Jun 22, 2023 |
| Contact name |
Andrew P Hutchins |
| E-mail(s) |
andrewh@sustech.edu.cn
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| Organization name |
Southern University of Science and Technology
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| Department |
Bioinformatics
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| Lab |
Bioinformatics and Genomics
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| Street address |
1088 Xueyuan Rd
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| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE213167 |
Factors controlling somatic reprogramming of transformed tumorigeneic cells to induced pluripotent-like stem cells [ATAC-seq] |
| GSE213225 |
Factors controlling somatic reprogramming of transformed tumorigeneic cells to induced pluripotent-like stem cells |
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| Relations |
| BioSample |
SAMN30809660 |
| SRA |
SRX17535201 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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