|
| Status |
Public on Mar 16, 2020 |
| Title |
Arcuate nucleus, Phf6_Input_Fasted_condition |
| Sample type |
SRA |
| |
|
| Source name |
Arcuate nucleus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6-7 weeks
genotype: wild type
feeding condition: Fasted
tissue: Arcuate nucleus
chip antibody: none
|
| Growth protocol |
Enriched ARC tissue dissected within 3 hours from 100 fed and 100 fasted wild-type mice (6-7 weeks old)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and PHF6-chromatin complexes were isolated with PHF6 antibody.
Libraries were prepared following the NEB/NEBNext® Library Quant Kit for Illumina®(E7630S). Amplified libraries were size-selected using a 2% gel to capture fragments between 200 bp and 500 bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Phf6_ChIPSeq_Fasted_condition_FoldEnrichment.bw
|
| Data processing |
ChIPseq reads were mapped to the mouse reference genome (GRCm38/mm10, downloaded from UCSC, http://genome.ucsc.edu/) using Bowtie 2 (version 2.2.9) with the following parameters: --local –X 2000.
Significant peaks were called using MACS2 (version 2.1.1.20160309) with “-f BAMPE” option and default threshold of q value (BH-adjusted p value) cutoff at 0.05.
The bedgrap file containing the signal ratio of ChIP to Input samples was acquired using MACS2 WITH “bdgcmp -m FE” option.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file containing the signal ratio of ChIP to input.
|
| |
|
| Submission date |
Jul 06, 2019 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Qian Li |
| E-mail(s) |
liqian@shsmu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Department |
Department of Anatomy and Physiology
|
| Street address |
280 South Chongqing Road, Building No.5, Room 408
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE133901 |
Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response [ChIP-Seq] |
| GSE139545 |
Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response |
|
| Relations |
| BioSample |
SAMN12226122 |
| SRA |
SRX6410187 |
