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| Status |
Public on Jun 24, 2024 |
| Title |
NanogN70+Oct4, Day10 |
| Sample type |
SRA |
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| Source name |
MEF
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| Organism |
Mus musculus |
| Characteristics |
cell line: MEF
cell type: Mouse embryonic fibroblast
reprogramming: NanogN70+Oct4
time point: Day10
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was harvested using TruePrep DNA Library Prep Kit V2 for Illumina kit (TD501-TD503, Vazyme),100000 cells per sample was used for sequencing libraries construction
Liarbries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (TD501-TD503, Vazyme)
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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 |
ATAC-seq was performed according to the previous study (Buenrostro et al., 2013, Buenrostro et al., 2015a). Briefly, a total of 50,000 cells were collected and incubated with 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) for 10 min on ice. The suspension of nuclei was centrifuged for 5 min at 500g at 4 °C, then resuspended in 50 μl transposition reaction mix (10 μl 5× TTBL, 5 μl TTE Mix V50 and 35 μl nuclease-free H2O) from the TruePrep DNA Library Prep Kit V2 for Illumina (TD501-TD503, Vazyme), and incubated at 37 °C for 30 min. DNA fragments were then PCR amplified and purified with a Qiaquick PCR (QIAGEN) column. Library concentration was detected by a VAHTS Human Genomic DNA Quantification and QC Kit (NQ201, Vazyme) according to the manufacturer’s protocol. Finally, libraries were indexed using TruePrep Index Kit V2 for Illumina (Vazyme, TD202), and sequencing was performed on Illumina Novaseq PE150 platform.
The ATAC-seq reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5), and SAMtools (v1.16.1) was used to remove the repetitive, low sequencing quality (mapq<30) and the mitochondrial DNA mapped reads in the total mapped reads. In order to make the data comparable between different sequencing depths, the signals were normalized to one million reads for each sample, and the value were further compressed into a binary format (bigWig) for downstream analysis and data visualization. Peak calling was performed using MACS (v1.4.2) with parameters as follows: -g mm --keep-dup all --nomodel --shiftsize 25.
Assembly: mm10
Supplementary files format and content: BigWig, Peaks&Summits bed
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| Submission date |
Sep 19, 2023 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Chengchen Zhao |
| E-mail(s) |
zhaochengchen@westlake.edu.cn
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| Organization name |
Westlake University
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| Lab |
Laboratory of Cell Fate Control
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| Street address |
Dunyu Road No.600, Xihu District
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310030 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE243513 |
Rational cell fate engineering through chromatin dynamics [ATAC-Seq] |
| GSE243517 |
Rational cell fate engineering through chromatin dynamics |
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| Relations |
| BioSample |
SAMN37452904 |
| SRA |
SRX21820622 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7789758_NanogN70_d10.bw |
151.1 Mb |
(ftp)(http) |
BW |
| GSM7789758_NanogN70_d10.peaks.bed.gz |
618.1 Kb |
(ftp)(http) |
BED |
| GSM7789758_NanogN70_d10.summits.bed.gz |
457.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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