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| Status |
Public on May 03, 2023 |
| Title |
ATAC_D0_1 |
| Sample type |
SRA |
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| Source name |
MEF
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| Organism |
Mus musculus |
| Characteristics |
strain: 129XOG2 E13.5 embryo
cell type: MEF
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| Treatment protocol |
Cells were cultured in indicated medium
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| Growth protocol |
riPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901. MEFs were cultured in MEF medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin (P/S). OG2 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1 x 10^5 cells were collected, washed once with cold DPBS. Then, cell nuclei were collected by lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) treating for 10 min on ice and centrifugation at 800 g at 4 ℃.
Fragmentation mix (10 μl 5X TTBL, 5 μl TTE Mix V50 and 35 μl ddH2O) was used for resuspending the cell nuclei followed by incubating at 37℃ for 30 min. Then, DNA fragments were purified by 100 μl VAHTS DNA Clean Beads (Vazyme). Purified DNA fragments were amplified by PCR for 15 cycles using the TruePrep Index Kit V2 (Vazyme). Finally, PCR products were purified by 60 μl VAHTS DNA Clean Beads. The ATAC-seq libraries were sequenced on the Illumina NovaSeq 6000 with read length of 150 bp.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.2.5) with options: --no-unal --no-mixed --no-discordant -X 2000 --local.
The null, not unmapped, and duplicated reads were removed by view and markdup functions in sambamba (v0.7.1) with default parameter settings and mitochondrial reads were removed by samtools.
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 --nomodel -f BAMPE --keep-dup all -g mm.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: peak text files
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| Submission date |
Nov 15, 2021 |
| Last update date |
May 03, 2023 |
| Contact name |
Yunkun Lu |
| Organization name |
Zhejiang University
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| Department |
Sir Run-Run Shaw Hospital
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| Street address |
3 Qingchun East Rd.
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310016 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE188824 |
Establish a rapid and efficient chemical reprogramming platform (ATAC-Seq) |
| GSE188834 |
Establish a rapid and efficient chemical reprogramming platform |
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| Relations |
| BioSample |
SAMN23163972 |
| SRA |
SRX13139341 |
| 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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