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Series GSE236234 Query DataSets for GSE236234
Status Public on Sep 09, 2024
Title LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [NAD-seq]
Organism Homo sapiens
Experiment type Other
Summary To investigate NADs associated DNAs in the naïve and primed hES cells.
 
Overall design In this study, we profiled for DNA loci within the nucleolus associated domain (NADs) in naïve and primed H9 hES cells for comparison. We followed a previously published “crosslinked method of nucleoli isolation” protocol described by Vertii et al. (Vertii et al. 2019).
Naïve and primed H9 hES cells maintained in RSeT and mTeSR, respectively, were collected for preparing NADs sequencing sample. 20-30 x 10^6 cells were subjected to ultrasonic cell disruption after crosslinking the cells. Nucleolar fraction was spin pelleted after 2-3 rounds of sonication in the high magnesium (HM) buffer and then subject to another round of sonication and nucleolar pelleting in the low magnesium (LM) buffer. The final pelleted nucleolar DNA were extracted and processed to DNA library preparation with the Illumina`s TruSeq DNA PCR-free Library Preparation kit (Illumina # 20015962), and 350 bp fragments were sonicated and size-selected by sample-purifying beads following manual instruction. The library was subjected to 150bp paired-end sequencing onNovaSeq. The details of protocol is described by by Vertii et al. (Vertii et al. 2019). More protocol details are described in the methods of this study.
 
Contributor(s) Zhang J, Huynh L, Ramalho-Santos M
Citation(s) 39413784
Submission date Jun 30, 2023
Last update date Dec 09, 2024
Contact name Juan Zhang
E-mail(s) tzzhangjuan@gmail.com
Organization name LTRI
Street address 25 Orde Street, Room 6-1001 MRS
City Toronto
State/province Ontario
ZIP/Postal code M5T 3H7
Country Canada
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (12)
GSM7520179 RSeT H9, rep1 Whole-cell DNA
GSM7520180 RSeT H9, rep1 Nucleolar DNA
GSM7520181 RSeT H9, rep2 Whole-cell DNA
This SubSeries is part of SuperSeries:
GSE232939 LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs
Relations
BioProject PRJNA989535

Download family Format
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Supplementary file Size Download File type/resource
GSE236234_simple_naive_NAD.bed.gz 328.2 Kb (ftp)(http) BED
GSE236234_simple_primed_NAD.bed.gz 160.0 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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