|
| Status |
Public on Aug 14, 2019 |
| Title |
ESCs, PmlKO_ATAC_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
genotype: Pml-/-
|
| Growth protocol |
E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 20% FBS, GlutaMAX (Gibco), MEM Non-Essential Amino Acids (Gibco), Leukemia inhibitory factor, 1 mM sodium pyruvate, penicillin/streptomycin, 0.1 mM 2-mercaptoethanol, 3 mM CHIR99021 and 1 mM PD0325901. Cells were cultured at 37 °C under 5% CO2 in air.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1 x 10e5 cells were used for each transposition reaction
The libraries were prepared by using the Illumina Nextera DNA Library Prep Kit, and size-selected to 200-500 bp using SPRIselect beads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive.
Non-uniquely mapping reads were filtered out using a MAPQ threshold of 30.
PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file was generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY
|
| |
|
| Submission date |
Aug 08, 2019 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Misuzu Kurihara |
| E-mail(s) |
kmisuzu1018@gmail.com, miyanari@nibb.ac.jp
|
| Organization name |
National Institute for Basic Biology
|
| Street address |
5-1 Higashiyama, Myodaiji
|
| City |
Okazaki |
| State/province |
Aichi |
| ZIP/Postal code |
444-8787 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE135561 |
ATAC-seq analyses with wild-type and PML KO mESCs |
| GSE135563 |
Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions |
|
| Relations |
| BioSample |
SAMN12532156 |
| SRA |
SRX6676096 |
