|
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 |