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Sample GSM6668770 Query DataSets for GSM6668770
Status Public on Jan 13, 2024
Title IECs_H3K27bu_ChIP_rep2
Sample type SRA
 
Source name Intestinal epithelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Cecal intestinal epithelial cells
treatment: None
antibody: H3K27bu (Millipore ABE2854)
Treatment protocol Mice were treated with vehicle (10g/L Splenda) and with or without 1g/L Ampicillin for 7 days. On day 7, mice were gavaged with either mock gavage (25% glycerol) or tributyrin for 6 hours prior to tissue harvest.
Extracted molecule genomic DNA
Extraction protocol Intestinal epithelial cells were isolated using DTT/EDTA mechanical disruption followed by Dispase dignestion. RNA was harvested using RNAeasy isolation kits and genomic DNA was isolated following immunoprecipitation of sonicated chromatin.
Libraries were generated using NEBNext Ultra II kits.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Transcript Quantification with Salmon (version 0.8.2)
Alignment of ChIPseq reads was done with Rsubread (version 1.30.6)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0)
Assembly: Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0)
Supplementary files format and content: fastq, bigwigs, counts
 
Submission date Oct 21, 2022
Last update date Jan 13, 2024
Contact name Leah Gates
E-mail(s) leah.gates@case.edu
Organization name Case Western Reserve University - Cleveland, OH
Street address Case Western Reserve University
City Cleveland
State/province Ohio
ZIP/Postal code 44106
Country USA
 
Platform ID GPL19057
Series (1)
GSE216319 Histone butyrylation in the mouse intestine is mediated by the microbiota and associated with regulation of gene expression
Relations
BioSample SAMN31407402
SRA SRX17989078

Supplementary file Size Download File type/resource
GSM6668770_IECs_H3K27bu_ChIP_rep2.bw 476.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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