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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-H3K27me3 |
| Sample type |
SRA |
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| Source name |
R1
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| Organism |
Mus musculus |
| Characteristics |
cell line: R1
cell type: ES cells
growth protocol: Serum+Lif
treatment: control
time: D8
chip antibody: H3K27me3 (Millipore #07-449)
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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 ESCs, with two rounds of 48 h treatments (2.5mM) between D1 and D3, D8 and D10
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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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| Description |
H3K27me3_D8.bw
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Libraries were aligned with bowtie2 with default parameter on mouse and fly genomes together. We filtered all alignment on MAPQ (mapping quality value) 30 with samtools . We deduplicated libraries with picard tool4. We used the number of reads mapped on fly genome as spike-in value and we downsampled libraries according to manufacturer instruction.
Genome_build: mm10
Supplementary_files_format_and_content: we merged the replicates by using mean values and generated bigwig coverage track
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| Submission date |
Jul 22, 2021 |
| 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 |
| GSE180680 |
HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [ChIP-Seq] |
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| Relations |
| BioSample |
SAMN20352120 |
| SRA |
SRX11525465 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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