|
| Status |
Public on Jul 28, 2023 |
| Title |
H3K4me1_ChIP_ESC2_WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
E14 mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E14 mouse embryonic stem cell
chip antibody: H3K4me1
genotype: wild type
treatment: dTAG-13
|
| Treatment protocol |
For the dTAG treatment, 2uM ofdTAG-13 (Tocris Bioscience) was added from day 1 of NPC differentiation and cells were harvested on day 4.
|
| Growth protocol |
Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP and input library preparation were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
k4me1_esc2_wt.bw
|
| Data processing |
The processed files (bigWig) were created using deepTools (Ramírez et al., 2016).
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Jul 27, 2023 |
| Last update date |
Jul 29, 2023 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
|
| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE160890 |
KMT2C/KMT2D (MLL3/MLL4) Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell Differentiation [ChIP-seq] |
| GSE160892 |
Mll3/Mll4 catalytic activity is necessary for de novo enhancer-promoter contacts during embryonic stem cell differentiation |
|
| Relations |
| BioSample |
SAMN36726534 |
| SRA |
SRX21171485 |
