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Sample GSM7398496 Query DataSets for GSM7398496
Status Public on May 24, 2024
Title rat_iOL_26c
Sample type SRA
 
Source name brain
Organism Rattus norvegicus
Characteristics tissue: brain
cell line: primary iOLs
cell type: oligodendrocytes
genotype: wildtype
treatment: 26C
antibody: H3K27ac
Extracted molecule genomic DNA
Extraction protocol ~5 million rat iOL were treated with vehicle or 26C and then crosslinked with 1% formaldehyde for 10 min at room temperature and lysed with 1× Nuclease Digest Buffer. Chromatin was digested by Enzyme Mix and sonicated using Covaris sonicator then processed with chromatin immunoprecipitation using the H3K27ac antibody
The DNA libraries were amplified using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645, New England Biolabs) according to its recommended protocol and sequenced by NovaSeq 6000 system on pair-end 2×150 bp mode
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing MAPS pipeline was used to analyze H3K27ac HiChIP data generated from control and 26C treated oligodendrocyte cells. Briefly, we mapped the raw fastq files to the reference genome rn5 using bwa-mem and kept only the uniquely mapped reads. We then kept paired-end reads where at least one end overlaps with the H3K27ac ChIP–seq peaks in the matched cell type and fitted a positive Poisson regression model to remove systematic biases including restriction enzyme cutting frequency, GC content, sequence uniqueness, and ChIP efficiency. We then identified significant long-range chromatin interactions as 10 kb bin pairs with FDR <1% and normalized chromatin contact frequency >2. Lastly, we assigned genes whose transcription start site resides in the anchor binsof MAPS-identified interactions
Assembly: rn5
Supplementary files format and content: txt file contains MAPS-identified interactions
Supplementary files format and content: txt file contains MAPS-identified interactions
Library strategy: HiChIP
 
Submission date May 19, 2023
Last update date May 24, 2024
Contact name XUEZHAO LIU
E-mail(s) xuezhao.liu@cchmc.org
Organization name cincinnati children's hospital medical center
Street address 3333 Burnet Ave. MLC 7013, T6.525
City cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL25947
Series (2)
GSE232954 Small-molecule-induced epigenetic rejuvenation overcomes myelinogenic barriers and stimulates myelin repair [HiChIP]
GSE232956 Small-molecule-induced epigenetic rejuvenation overcomes myelinogenic barriers and stimulates myelin repair
Relations
BioSample SAMN35220422
SRA SRX20454193

Supplementary file Size Download File type/resource
GSM7398496_rat_Rn5_OL_26C_H3K27Ac_HichIP.txt.gz 618.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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