|
| Status |
Public on May 24, 2022 |
| Title |
FoxO1_S961_Refeed |
| Sample type |
SRA |
| |
|
| Source name |
liver tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57BL/6
chip antibody: GFP (Abcam, ab290)
treatment: 4-h-fasted / 1-h-refeed S961 treated
|
| Treatment protocol |
Samples were treated by vehicle or S961 for 48hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicatd nuclei and GFP- or histone-DNA complexes were isolated with antibody
ChIP-seq libraries were constructed using KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instructions. ChIP-seq libraries were quantified by Tapestation (Agilent) and sequenced on an Illumina NEXTseq (Illumina, San Diego, CA, USA) with 75-base single-end mode.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to mouse genome mm10 using Bowtie2
The reads used in subsequent analysis passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome. Duplicate reads were removed with Picard tools. The tags were extended at their 3′-ends to 200-bp.
Peak calling was performed by MACS 2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tdf files were generated using igvtools
|
| |
|
| Submission date |
Jun 01, 2020 |
| Last update date |
May 24, 2022 |
| Contact name |
Domenico Accili |
| Organization name |
Columbia University
|
| Department |
Medicine
|
| Street address |
1150 ST NICHOLAS AVENUE, RM238
|
| City |
NEW YORK |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE151544 |
Characterization of chromatin and gene expression changes during fasting and refeeding in mouse liver [ChIP-Seq] |
| GSE151546 |
Characterization of chromatin and gene expression changes during fasting and refeeding in mouse liver |
|
| Relations |
| BioSample |
SAMN15074606 |
| SRA |
SRX8439658 |
