|
Status |
Public on May 18, 2021 |
Title |
ESCs, Jun-ChIP-seq.8h |
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 treatment: treated with doxycycline for 8h chip antibody: Abcam, ab31419
|
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 |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
bcl2fastq conversion software v2.17 used for basecalling. The ChIP-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 18, 2021 |
Contact name |
kuang junqi |
E-mail(s) |
kuangjunqi@westlake.edu.cn
|
Organization name |
westlake University
|
Street address |
No.18 Shilongshan Road
|
City |
hangzhou |
ZIP/Postal code |
310024 |
Country |
China |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE135396 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 1] |
GSE135451 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation |
|
Relations |
BioSample |
SAMN12497456 |
SRA |
SRX6657515 |