|
| Status |
Public on Dec 21, 2016 |
| Title |
Nrf1_ChIP-seq_MEF_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type MEFs immortalized with SV40 large T antigen and treated with MG132.
|
| Organism |
Mus musculus |
| Characteristics |
chip-antibody: Cell Signaling Technology, anti-TCF11 (D5B10)
cell type: Mouse enbryonic fibroblasts
|
| Treatment protocol |
MEFs were treated with 10 μM of MG132 for 6 hr.
|
| Growth protocol |
MEFs were maintained in DMEM supplemented with 10% FBS and antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated using antibody to Nrf1 and Dynabeads-proteinA and -proteinG
Libraries were prepared according to NuGEN's instructions accompanying the Ovation Ultralow DR Multiplex System 1-8 (NuGEN, 0330-32).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP samples using antibody to Nrf1 obtained from MG132-treated wild-type MEFs, replicate 1
|
| Data processing |
ChIP-seq reads were aligned to the mm9 genome assembly using bwa version 0.6.2-r126.
Data were filtered using samtools version 0.1.18
Peaks were called using macs2 version 2.0.10
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated using BEDtools version 2.17.0 and UCSC Genome Bioinformatics
|
| |
|
| Submission date |
Oct 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Eri H Kobayashi |
| Organization name |
Tohoku University Graduate School of Medicine
|
| Department |
Medical Biochemistry
|
| Street address |
2-1 Seiryo-machi, Aobaku
|
| City |
Sendai |
| State/province |
Miyagi |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE89344 |
A Homeostatic Shift Facilitates Endoplasmic Reticulum Proteostasis through Transcriptional Integration of Proteostatic Stress Response Pathways [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN05956186 |
| SRA |
SRX2311119 |
