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| Status |
Public on Jun 01, 2020 |
| Title |
WT_Flavopiridol_1h_Dhx9_4C_rep1 |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: V6.5
cell type: mouse embryonic stem cells
treatment: Flavopiridol treated mES
restriction enzyme: AluI
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| Treatment protocol |
All degron mES cells were pre-treated with 1 μg/ml Doxycycline for 12 hours. For the time course of Pol II degron, IAA was treated with or without 500 μM indole-3-acetic acid (IAA) 1 hour and 6 hours respectively. For wild type mES cells treated with transcription inhibitors, Actinomycin D, Flavoporidol was used with 1 μM for 1 hour and DRB was used with 100 μM for 1 hour. Etoposide was used with 10 μM for 1 hour.
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| Growth protocol |
The V6.5 mouse ES (mES) cell line was cultured with irradiated mouse embryonic fibroblasts in DMEM-KO containing 15% FBS, leukaemia inhibiting factor (LIF), L-glutamine, β-mercaptoethanol, non-essential amino acids and penicillin/ streptomycin at 37 ℃ with 5% CO2, and passage twice for experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We modified 4C-seq protocol based on 3C-HTGTS version (Jain et al., 2018). Briefly, After Nla III digestion and proximal ligation, target DNA was extracted with biotinyled bait primer.
Library are constructed via two rounds of PCR with truseq adaptor.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Library strategy: 4C-seq
Linker detection: The paired-end reads were demultiplexed with fastq-multx (Version: 1.3.1), enzyme site was trimmed using trimlinker form ChIA-PET2 software, read pairs containing at least one enzyme site and bait sequences were selected.
Reads alignment: The selected reads were mapped to the mm10 genome with bowtie2 using the parameter “--very-sensitive-local -L 30 --score-min G,20,8”.
Filtering: Discard read-pairs marked as multihits, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, dangling-end and PCR artefacts.
Normalization: Final bam files were converted into wig file with pyicos, and then the wig files were performed quantile normalization with DANPOS2
The distributions of normalized contact intensities were put into bigwig files for visualization using the UCSC genome browser mm10.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files were generated using wigToBigWig, which the total tags are normalized to equal.
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| Submission date |
Feb 24, 2020 |
| Last update date |
Jun 02, 2020 |
| Contact name |
Xiong Ji |
| E-mail(s) |
xiongji@pku.edu.cn
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| Organization name |
Peking University
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| Department |
School of Life Sciences
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| Lab |
Jilab
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| Street address |
Haidian District, Beijing Summer Palace Road No. 5
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE145784 |
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [4C-seq] |
| GSE145874 |
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III |
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| Relations |
| BioSample |
SAMN14168382 |
| SRA |
SRX7786012 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4332971_WT_Flavopiridol_1h_Dhx9_4C_rep1.bw |
80.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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