|
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
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|
|
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 |