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| Status |
Public on Feb 01, 2019 |
| Title |
RNA-Seq of WT and constitutively methylated mESCs |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
WT J1 and 3B3L cells (in which Dnmt3B and Dnm3L are constitutively expressed from an exogenous construct) were cultured under both serum/LIF and 2i/LIF conditions. 3B3L cells do not show ground state-associated hypomethylation phenotype. This experiment sought to analyse the gene expression changes between the two conditions.
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| Overall design |
Three biological replicates per condition J1 serum, J1 2i, 3B3-3l serum, 3B3-3l 2i.
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| Contributor(s) |
McLaughlin K, Flyamer IM, Thomson JP, Mjoseng HK, Shukla R, Williamson I, Grimes GR, Illingworth RS, Adams IR, Pennings S, Bickmore WA, Meehan RR |
| Citation(s) |
31722211, 32585002 |
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Katy A McLaughlin, Ilya M Flyamer, John P Thomson, Heidi K Mjoseng, Ruchi Shukla, Iain Williamson, Graeme R Grimes, Robert S Illingworth, Ian R Adams, Sari Pennings, Richard R Meehan, Wendy A Bickmore. DNA methylation directs polycomb-dependent 3D genome re- organisation in naive pluripotency. bioRxiv 527309. doi:10.1101/527309
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| Submission date |
Oct 12, 2018 |
| Last update date |
Nov 16, 2020 |
| Contact name |
Graeme Richard Grimes |
| E-mail(s) |
graeme.grimes@ed.ac.uk
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| Organization name |
University of Edinburgh, The Institute of Genetics and Cancer
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| Department |
Human Genetics Unit
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| Lab |
Bioinformatics Analysis Core
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| Street address |
Western General Hospital, Crewe Road
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| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
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| Platforms (1) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA495937 |
| SRA |
SRP165285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE121171_RAW.tar |
14.8 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE121171_txisailfishrawcounts.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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