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Sample GSM4007593 Query DataSets for GSM4007593
Status Public on May 18, 2021
Title ESCs, Dox.12h.ATAC
Sample type SRA
Source name mouse embryonic stem cells (mESCs)
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: 12h
Treatment protocol Treated with 2µg/ml doxycycline
Growth protocol Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)
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.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
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
Submission date Aug 05, 2019
Last update date May 19, 2021
Contact name kuang junqi
Organization name westlake University
Street address No.18 Shilongshan Road
City hangzhou
ZIP/Postal code 310024
Country China
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
BioSample SAMN12497415
SRA SRX6657480

Supplementary file Size Download File type/resource 130.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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