|
| Status |
Public on May 08, 2016 |
| Title |
Myc-Dnmt1 wt ESC [ChIP-seq] |
| Sample type |
SRA |
| |
|
| Source name |
ES cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
cell type: embryonic stem cells (ESCs)
genotype/variation: Exogenous Myc-tagged Dnmt1 expressed
chip antibody: anti Myc-tag antibody (CST, 9B11, mouse mAb)
molecule subtype: Crosslinked chromatin
|
| Growth protocol |
Standard condition for ES cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using QIAGEN All-prep kit
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina. Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
ESCs were corsslinked with 1% formaldehyde and after nuclear lysis, chromatin was sheared by sonication (30s on/off, 15 cycles) and immunoprecipitated with an anti-Myc tag antibody (CST, 9B11) using Protein A + G magnetic beads (Millipore)
|
| 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: Whole genome mapped read counts normalized by the total mapped reads and genome size (mapped reads per kilobase genome per million reads). Mapped reads per kilobase
|
| |
|
| Submission date |
Feb 10, 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 (2) |
| GSE77779 |
Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing [ChIP-seq] |
| GSE77781 |
Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing |
|
| Relations |
| BioSample |
SAMN04485141 |
| SRA |
SRX1569974 |
