|
| Status |
Public on May 31, 2021 |
| Title |
ESCs, BRD7-ChIP-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: BRD7 (Proteintech, 51009-2-AP)
|
| 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 |
Protein-DNA complexes were isolated with antibody and Tn5-proteinA/G.
The ChIP DNA library for sequencing was constructed with NovoNGS CUT&Tag 2.0 High-Sensitivity Kit for Illumina (novoprotein) according to manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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 (GRCm38)
Supplementary_files_format_and_content: bigWig files
|
| |
|
| Submission date |
May 30, 2021 |
| Last update date |
May 31, 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 |
GPL24247 |
| Series (2) |
| GSE135451 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation |
| GSE175818 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 3] |
|
| Relations |
| BioSample |
SAMN19459940 |
| SRA |
SRX11030059 |
