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SRX19275007: GSM7024535: E17_H3K4me3; Mus musculus; OTHER
1 ILLUMINA (Illumina HiSeq 4000) run: 21.8M spots, 3.3G bases, 796.1Mb downloads

External Id: GSM7024535_r1
Submitted by: Bartolomei Lab, Cell and Developmental Biology, University of Pennsylvania
Study: TET1 catalytic activity is required for reprogrammign of imprinting control regions and the patterning of sperm-specific hypomethylated regions [CUT&RUN]
show Abstracthide Abstract
DNA methylation erasure is required for mammalian primordial germ cell reprogramming. TET enzymes iteratively oxidize 5-methylcytosine to generate 5-hyroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxycytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during germline reprogramming remains unresolved due to the lack of genetic models that decouple TET1 activities. Here, we generated two mouse lines expressing catalytically inactive TET1 (Tet1-HxD) and TET1 that stalls at 5hmC (Tet1-V). This experiment was done to conduct genome wide DNA methylation profiling of catalytically inactive Tet1HxD/HxD sperm, 5hmC stalling Tet1V/V sperm, KO Tet1-/- sperm, and WT sperm. Sperm samples were collected from adult males (>10 week). E17.5 WT prospermatogonia were collected using FACS of Oct4-GFP cells and CUT&RUN for H3K4me3 and IgG were done on 130,000 cells. Overall design: 130,000 freshly sorted E17.5 Oct-GFP+ prospermatogonia cells were used for H3K4me and IgG CUT&RUN
Sample: E17_H3K4me3
SAMN33053833 • SRS16676708 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7024535
Instrument: Illumina HiSeq 4000
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Freshly sorted cells were bound to concanavalin A-coated magenetic beads and wash and permeabilize using C&R Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, with 1x Roche complete protease inhibitor EDTA Free) with 0.05% Digitonin and 2 mM EDTA CUT&RUN libraries were prepared using KAPA HyperPrep Kit and was ammplified using KAPA HiFi Hot Start Ready mix. All of DNA that was recovered following Phenol:Chloroform extraction was used as input.
Runs: 1 run, 21.8M spots, 3.3G bases, 796.1Mb
Run# of Spots# of BasesSizePublished
SRR2333282221,789,8183.3G796.1Mb2024-02-26

ID:
26498033

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