|
| Status |
Public on Jan 10, 2017 |
| Title |
Input D6 |
| Sample type |
SRA |
| |
|
| Source name |
NT2/D1_RA_input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NT2/D1
cell type: embryonal carcinoma cells
treated with: 10 μM all trans retinoic acid for 6 days
chip anibody: none
|
| Growth protocol |
NT2/D1 cells were cultured in Dulbecco’s modified Eagle’s minimum essential medium (DMEM; Wako) supplemented with 10% (v/v) fetal bovine serum (FBS). For retinoic acid treatment, NT2/D1 cells were treated with 10 μM all trans retinoic acid (RA; Wako)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with ChIP-IT Express Enzymatic kit (Active motif) according to the manufacturer's instructions with some modifications. Briefly, cells were fixed with 1% formaldehyde for 10 min at room temperature. After enzymatic chromatin digestion, we performed sonication (5X30 sec) using the Bioruptor (Diagenode).
ChIP-seq libraries were constructed with NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RTA v2.1.3.0 was used for base-calling.
Raw fastaq files were processed using FASTQ groomer v1.0.4 with default setting.
ChIP-seq reads were mapped to the human hg19 genome uging botie2 v2.2.6 with default setting.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using SraTailor software v1.0.0 with default setting.; The y-axis indicates RPM (reads per million) values.
|
| |
|
| Submission date |
Apr 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ko Ishihara |
| E-mail(s) |
[email protected]
|
| Phone |
+81-96-373-6820
|
| Organization name |
Kumamoto University
|
| Department |
Priority Organization for Innovation and Excellence
|
| Street address |
2-2-1 Honjyo
|
| City |
Kumamoto |
| ZIP/Postal code |
860-0811 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE80705 |
Removable insulator facilitates higher-order chromatin remodeling and selective gene expression in the HOXA locus via the retinoic acid signaling [ChIP-seq] |
| GSE80706 |
Removable insulator facilitates higher-order chromatin remodeling and selective gene expression in the HOXA locus via the retinoic acid signaling |
|
| Relations |
| BioSample |
SAMN04904279 |
| SRA |
SRX1728901 |
