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Sample GSM7091017 Query DataSets for GSM7091017
Status Public on Mar 20, 2023
Title Mouse Liver tumor, Nrf2 KO, AcH3K27, rep2
Sample type SRA
 
Source name Liver tumor
Organism Mus musculus
Characteristics Sex: male
tissue: Liver tumor
genotype: Knockout Nrf2-/-
chip antibody: AcH3K27
Growth protocol Male Nrf2 wild type or knockout mice were were treated with hepatic carcinogen diethylnitrosamine (DEN) (25 mg/kg body weight) via intraperitoneal injection at 14-day-old to initiate tumor formation. At the 36 weeks post-DNE treatment, mice were sacrificed for liver tumor collection.
Extracted molecule genomic DNA
Extraction protocol Liver tumor tissues were crosslinked with 1% formaldehyde, sonicated, and immunoprecipitated with AcH3K27 antibody.
10 ng ChIP pulldown DNA was prepared for the library using TruSeq ChIP Sample Preparation kit (Illumina). Libraries were amplified using 18 cycles on the thermocycler, followed by size selection at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Mouse Liver tumor_AcH3K27_EMDMillipore
Data processing ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
reads were mapped with Bowtie2 and analyzed by MACS2 for the peak calling
Assembly: mm10
Supplementary files format and content: bigWig
 
Submission date Mar 10, 2023
Last update date Mar 21, 2023
Contact name Xingguo Zhu
E-mail(s) zhughsu@gmail.com
Phone 7067216301
Organization name Augusta University
Department Cancer Center
Street address 1120 15th st, CN4114, CN4114
City Augusta
State/province Georgia
ZIP/Postal code 30912
Country USA
 
Platform ID GPL19057
Series (1)
GSE227068 Nrf2 drives hepatocellular carcinoma progression through acetyl-CoA-mediated metabolic, epigenetic and oncogenic regulatory networks
Relations
BioSample SAMN33710161
SRA SRX19631183

Supplementary file Size Download File type/resource
GSM7091017_Nrf2_KO-AcH3K27-S2.bw 286.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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