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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 18, 2021 |
| Title |
ESCs, Dox.8h.ATAC |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells (mESCs)
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| Organism |
Mus musculus |
| Characteristics |
cell type: OG2 transgenetic mouse embryonic stem cells (OG2ES)
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
genotype: c-Jun_TetOn_mESC
agent: Dox
time: 8h
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| Treatment protocol |
Treated with 2µg/ml doxycycline
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| Growth protocol |
Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers 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 |
bcl2fastq conversion software v2.17 used for basecalling.
The ATAC-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
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| Submission date |
Aug 05, 2019 |
| Last update date |
May 19, 2021 |
| Contact name |
kuang junqi |
| E-mail(s) |
kuangjunqi@westlake.edu.cn
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| Organization name |
westlake University
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| Street address |
No.18 Shilongshan Road
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| City |
hangzhou |
| ZIP/Postal code |
310024 |
| Country |
China |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE135395 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ATAC-Seq] |
| GSE135451 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation |
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| Relations |
| BioSample |
SAMN12497416 |
| SRA |
SRX6657479 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4007592_Dox.8h.ATAC.bw |
67.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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