|
| Status |
Public on Nov 09, 2017 |
| Title |
panCBFB_total |
| Sample type |
SRA |
| |
|
| Source name |
Adult total thymocyte
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Adult total thymocyte
antibody: pan-Cbfb
|
| Treatment protocol |
Cells were subjected to crosslinking and nuclei were lysed. Nuclei sample was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON). Sonicated chromatin was incubated overnight at 4 °C with magnetic beads-attached anti-Cbfb1, anti-Cbfb2, or pan-Cbfb polyclonal antibodies that were generated in our laboratory. Immunoprecipitated DNA was then purified.
|
| Growth protocol |
Lineage negative liver cells were derived from E12.5 fetus and total thymocytes were derived from 4-6 wk old mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-seq Library prep Kit (E6240). The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Pan-Cbfb ChIP-seq of total thymocytes
|
| Data processing |
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumlated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file format of mapped reads per kilobase
|
| |
|
| Submission date |
Dec 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
|
| Organization name |
RIKEN
|
| Department |
IMS
|
| Lab |
Laboratory for Integrative Genomics
|
| Street address |
1-7-22 Suehiro, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE90794 |
Genome-wide maps of Cbfb variants bound regions in E12.5 lineage negative fetal liver cells and adult thymocytes. |
|
| Relations |
| BioSample |
SAMN06099208 |
| SRA |
SRX2389674 |
