|
| Status |
Public on Aug 18, 2023 |
| Title |
flox_Liver_input |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: floxed Fbxw7 (WT)
strain: C57BL/6J
Sex: male
treatment: Fasted 24h
chip antibody: none
|
| Treatment protocol |
Flox and liver-specific Fbxw7 KO (Fbxw7 LKO) on a C57BL/6J background were fasted 24h prior to liver isolation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Livers were crosslinked with 1% formaldehyde for 12 minutes followed by sonication (200-500 bp enrichment). Each ChIP-seq sample consisted of a pool of three independent ChIP samples each prepared using 2 mouse livers.
ChIP DNA libraries were prepared using the NEB Ultra II DNA library preparation kit according to Illumina recommendations.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic v0.36.
Paired-end cleaned reads were mapped to the mouse reference genome (mm10) using BWA-MEM v0.7.12 with default parameters.
Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1.
Peaks were called using MACS2 software suite v2.1.1.20160309 at an an FDR alpha < 0.05 followed by subsequent filtering to FDR < 0.001 using sequenced libraries of input DNA as control. Peaks in mitochondrial chromosome and scaffold regions were removed.
Peak annotations were performed using the annotatePeaks.pl command from HOMER software suite v4.11.1.
Assembly: mm10
Supplementary files format and content: bigwig (.bw) files for each sample
Supplementary files format and content: tab-delimited text files of annotated ERRa peaks for both flox and Fbxw7 LKO 24h-fasted mice using respective inputs as controls
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Aug 18, 2023 |
| Contact name |
Vincent Giguère |
| E-mail(s) |
vincent.giguere@mcgill.ca
|
| Phone |
514-398-5899
|
| Organization name |
McGill University
|
| Department |
Goodman Cancer Centre
|
| Street address |
1160 Pine Ave West, McIntyre Bldg Room 710
|
| City |
Montréal |
| State/province |
QC |
| ZIP/Postal code |
H3A 1A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE205845 |
Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression |
| GSE205847 |
Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression |
|
| Relations |
| BioSample |
SAMN28964715 |
| SRA |
SRX15672329 |
