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Status |
Public on May 31, 2023 |
Title |
Npc1-/- mouse O4+ cells H3K27me3 |
Sample type |
SRA |
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|
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).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
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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
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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 |