|
| Status |
Public on Aug 11, 2020 |
| Title |
NOD ES cells H3K4me3 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
NOD ES cells H3K4me3 ChIP
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOD
cell type: Embryonic stem cells
mark: H3k4me3
chip antibody: anti-H3K4me3, Abcam ab8580, lot GR240214-2
|
| Treatment protocol |
ES cells were grown in the presence of 2i
|
| Growth protocol |
Cells were isolated from mouse embryos
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
embryonic stem cells were isolated from embryos and analyzed using ChIP-Seq
ES cells were crosslinked with formaldehyde, then sonicate to fragment chromatin, and then subjected to antibody against perspective histone modification
ChIP DNA was end-repaired, then phosphorylated and an A was added. Illumina adapters were ligated and then PCR amplified to generate the sequencing library.
ChIP-Seq libraries were sequenced on Illumina HiSeq2500 at single-end 50-bp (base pair), resulting 25-30 million reads per library)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling softwares version was HiSeq Control Software 2.2.38 and RTA 1.18.61
BCL files to fastq files conversion and demultiplexing were done using CASAVA v1.8.2
Reads are aligned to reference genome using STAR (v2.2.0c)
Genome_build: mm9
Supplementary_files_format_and_content: Homer annotated peak file
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Manching Ku |
| Organization name |
Medical Center - University of Freiburg
|
| Department |
Hematology and Oncology
|
| Street address |
Mathildenstrasse 1
|
| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE154458 |
Premature activation of immune transcription programs in autoimmune-predisposed mouse embryonic stem cells and blastocysts |
| GSE155046 |
Premature activation of immune transcription programs in autoimmune-predisposed mouse embryonic stem cells and blastocysts |
|
| Relations |
| BioSample |
SAMN15541795 |
| SRA |
SRX8734961 |
