NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6764930 Query DataSets for GSM6764930
Status Public on May 31, 2023
Title Npc1-/- mouse O4+ cells H3K27me3
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics tissue: brain
cell line: primary cells
cell type: O4+ oligodendrocyte
genotype: Npc1-/-
chip antibody: H3K27me3 (ActiveMotif; 39155)
Extracted molecule genomic DNA
Extraction protocol Cells were isolated from brains of 16-day-old mice by magnetic-activated cell sorting using microbeads targeting the antigen O4 and were immediately flash frozen. Cell pellets from 6 mice were pooled together and fixed with 1% formaldehyde for 15 minutes and quenched with glycine. After cell lysis, chromatin was sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K, and heat, followed by ethanol precipitation. Soluble chromatin for H3K27me3 ChIP-seq was spiked-in with soluble Drosophila chromatin equivalent to 5-10% of mouse chromatin. The mix of suble chromatin was incubated with 4 ug of antibody against H3K27me3 or H3K27ac. Complexed were eluted with SDS buffer. ChIP-DNA was purified with phenol-chloroform extraction. *Drosophila spike-in was used for H3K27me3, but not H3K27ac
libraries were prepared by consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. These steps were done with an automated system (Apollo 342, Wafergen Biosystems/Takara).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description ChIP-seq for H3K27me3 performed on O4-positive cells (oligodendrocyte lineage) collected from mice lacking functional NPC1 at 16-days of age. Cells from 6 mice were pooled together for a single analysis
Data processing Reads were alligned using the Burrows-Wheeler Aligner algorithm on default settings
Duplicate reads were removed and uniquely mapped reads with a mapping quality score of at least 25 were used.
The number of test tags were normalized for each sample with Drosophila spike-in tags
Alignments were extended in silico at their 3'-ends to a length of 200bp and assigned to 32-nt bins along the genome. The resulting histograms were stored as BigWigs.
Assembly: mouse mm10
Supplementary files format and content: BigWig
 
Submission date Nov 29, 2022
Last update date May 31, 2023
Contact name Andrew Lieberman
Organization name University of Michigan
Department Pathology
Street address 1150 W Medical Center Drive
City Ann Arbor
State/province MI
ZIP/Postal code 48105
Country USA
 
Platform ID GPL19057
Series (2)
GSE219007 The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells ChIP-seq
GSE221610 The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells
Relations
BioSample SAMN31929264
SRA SRX18415048

Supplementary file Size Download File type/resource
GSM6764930_4_0D47_01RQUM_NPC-IV-VI_H3K27me3_mm10_i33_dmnorm_signal.bw 148.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap