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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 17, 2023 |
| Title |
ChIP-D8-rep1-Zfp57 |
| Sample type |
SRA |
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| Source name |
ES R1
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| Organism |
Mus musculus |
| Characteristics |
chip antibody: Zfp57 ( Abcam #ab45341)
treatment: ML-792
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| Treatment protocol |
We used ML-792, a highly selective inhibitor of the SUMO E1 enzyme, to decrease the global level of SUMOylation in mouse ES cells between D1 and D3. ChIP-seq were performed at D1 and D8 after SUMO recovery.
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| Growth protocol |
Serum+Lif
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
10min formaldehyde fixation followed by sonication . Immunoprecipitation was performed using ChIP-IT kit (#53040, Active Motif) following manufacturer's protocol. Experiments were done in duplicates.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from <1 ng to 10ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + --- cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamCoverage (bin size = 1)
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| Submission date |
Mar 07, 2022 |
| Last update date |
Mar 17, 2023 |
| Contact name |
Yann Loe-Mie |
| E-mail(s) |
Yann.loe-mie@pasteur.fr
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| Organization name |
Institut Pasteur
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| Department |
Computational Biology
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| Lab |
Bioinformatics and Biostatistics HUB
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| Street address |
25 rue du Dr Roux
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| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE180489 |
HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure |
| GSE198025 |
HypoSUMOylation in embryonic stem cells generate head-trunk embryo-like structures [ChIP-seq] |
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| Relations |
| BioSample |
SAMN26503613 |
| SRA |
SRX14394948 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5936104_ChIP-D8-rep1-Zfp57.bw |
450.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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