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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 17, 2023 |
| Title |
mC-D8-rep3 |
| Sample type |
SRA |
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| Source name |
R1
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| Organism |
Mus musculus |
| Characteristics |
cell line: R1
growth protocol: Serum+Lif
treatment: control
cell type: ES cells
time: D8
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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 (D1, D3, D8, D10), N2B27+Lif+PD0325901+CHIR99021 (2i)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using the Quick-DNA Midiprep plus kit from Zymo Research (#D4075)
The library construction was performed using the NEBNext Enzymatic Methyl-seq kit from New England Biolabs (#E7120S).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Bisulfite libraries were processed with the Bismark pipeline1 using bowtie2 aligner2 with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tabular file (chrom, start, strand, reads methyl, reads unmethyl)
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| Submission date |
Jul 21, 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 |
| GSE180597 |
HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [Methyl-seq] |
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| Relations |
| BioSample |
SAMN20343707 |
| SRA |
SRX11516588 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5465756_mC-D8-3_CG.bed.gz |
94.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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