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Series GSE98517 Query DataSets for GSE98517
Status Public on Jun 06, 2017
Title Activation of Lineage-Regulators and Transposable Elements Across a Pluripotent Spectrum
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Embryonic stem cells (ESC) are characterised by the pluripotent capacity to generate all embryonic lineages. Here we show ESC can occupy a spectrum of distinct transcriptional and epigenetic states in response to varied extrinsic conditions. This spectrum broadly corresponds to a developmental continuum of pluripotency and is coupled with a gradient of increasing global DNA methylation. Each pluripotent state is linked with activation of distinct classes of transposable elements (TE), which in turn influence ESC through generating chimeric transcripts. Moreover, varied ESC culture parameters differentially license activation of master lineage-regulators, including Sox1, Gata4 or Blimp1, and influence differentiation. The activation of Blimp1 is prevalent in 2i (without-LIF) conditions, and marks a dynamic primordial germ cell (PGC)-like sub-state, that is directly repressed by Klf4­ downstream of LIF/STAT3 signalling. Thus, extrinsic cues establish a spectrum of pluripotent states, in part by modulating sub-populations, as well as directing the transcriptome, epigenome, and TE.
Overall design Replicate RNA-seq and Methyl-seq datasets from mESC (129 or B6 background), maintained in multiple pluripotent culture parameters.
Contributor(s) Hackett JA
Citation(s) 28591649
Submission date May 03, 2017
Last update date Jul 25, 2021
Contact name Charles Bradshaw
Organization name University of Cambridge
Department Gurdon Institute
Street address Tennis Court Road
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (54)
GSM2598091 2i – N2B27_129_Rep1
GSM2598092 2i – N2B27_129_Rep2
GSM2598093 2i – N2B27_BL6_Rep1
BioProject PRJNA385325
SRA SRP106356

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE98517_RAW.tar 3.9 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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