|
| Status |
Public on Jun 29, 2020 |
| Title |
F9 undifferentiated ChIP |
| Sample type |
SRA |
| |
|
| Source name |
F9_UD_ChiP
|
| Organism |
Mus musculus |
| Characteristics |
cell line: F9
cell type: embryonal carcinoma cells
cell status: undifferentiated
chip antibody: K4me1
|
| Growth protocol |
F9 embryonal carcinoma cells were cultured and maintained in gelatin-coated tissue culture plates. Differentiation was induced by plating 20X106 cells in low attachment 15 cm petri dishes and the addition of 1µM Retinoic acid
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from crosslined using a standard phenol:chloroform extraction, followed by ethanol precipitation.
NEXTflex® ChIP-Seq Kit from Bioo Scientific
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
035883_F9-UD-K4me1_S69
|
| Data processing |
FastQC v.0.11.3 was used to observe read quality
TrimGalore for data trimming
Bowtie 2.3.3 to align data
Filter the BAM file to keep the reads with minimum MAPing Quality (MAPQ) 10.
Peak calling with epic2 using Input-ChIP pairs.
Peak annotations and visualizations through ChIPseeker R-package.
Genome_build: GRCm38.93
Supplementary_files_format_and_content: bedGraph and Excel
|
| |
|
| Submission date |
Aug 01, 2019 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Humaira Gowher |
| E-mail(s) |
[email protected]
|
| Organization name |
Purdue University
|
| Department |
Department of Biochemistry
|
| Street address |
175 South University St.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47906 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE135225 |
Oct4-mediated inhibition of Lsd1 activity promotes the active and primed state of pluripotency enhancers [ChIP-seq] |
| GSE135227 |
Oct4-mediated inhibition of Lsd1 activity promotes the active and primed state of pluripotency enhancers |
|
| Relations |
| BioSample |
SAMN12421208 |
| SRA |
SRX6632016 |
