|
| Status |
Public on Jan 04, 2016 |
| Title |
Nup98HoxA9 ES / anti-Crm1_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
EB3-derived Nup98-HoxA9 Expressing Stable cell line
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
chip antibody: Crm1 (Novus Biologicals, NB100-79804)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cross-linked chromatin was sheared by sonication, and MNase treatment.
To repair ChIP-DNA and Input-DNA ends, T4 DNA polymerase, Klenow enzyme and T4 polynucleotide kinase were used (New England Biolabs), and an A base was subsequently added to the 3'-end by the treatment of Klenow exo-. The adaptor ligation and the PCR amplification for 18 cycles of DNA fragments were performed with Illumina (PCR primer InPE1.0 & InPE2.0).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
illumina HCS2.0.5
ChIP-seq reads were aligned with the mouse reference geneme (mm9) using the bowtie program (v1.12.7) with the following parameters: -m 1 -v 3.
Duplicate reads were removed using samtools (v0.1.18).
The normalized ChIP-seq signal was calculated by subtracting the Reads Per Million mapped reads (RPM) of the Input signal from the IPed signal.
The signals were calculated at "window-size" bp genomic intervals with "step-size" bp window (e.g., The file name preffix of "w10000s1000" in our processed data means that the window-size is 10,000 bp and the step-size is 1,000 bp. )
genome build: mm9
processed data files format and content: bigWig files were generated for processed data containing chromosome, regions
|
| |
|
| Submission date |
May 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Masahiro Oka |
| Organization name |
National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)
|
| Lab |
Laboratory of Nuclear Transport Dynamics
|
| Street address |
7-6-8 Saito-Asagi
|
| City |
Ibaraki |
| State/province |
Osaka |
| ZIP/Postal code |
567-0085 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE68783 |
Genome-wide mapping of Nup98HoxA9- and Crm1-binding sites in ES cell lines. |
|
| Relations |
| BioSample |
SAMD00029142 |
| SRA |
DRX030665 |
