|
| Status |
Public on Jun 07, 2023 |
| Title |
Rax-GFP ESCs, H3K27ac antagonist Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
ESC-derived eye organoids (Rax-GFP ESCs)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: eye organoid
cell type: retina progenitors
genotype: Rax-GFP knockin Het
antibody: Acetyl-Histone H3 (Lys27) (Cell Signaling technology, #8173S)
|
| Growth protocol |
DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using Bowtie2 version 2.4.5
Peak calling and bigWig generation was performed using HOMER v4.10.4
Assembly: mm10
Supplementary files format and content: bigWig files
|
| |
|
| Submission date |
Feb 06, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
NOZOMU TAKATA |
| E-mail(s) |
nozomu.takata@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Center for Vascular and Developmental Biology
|
| Street address |
303 East Superior Street, 10-220
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE202759 |
Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis. |
| GSE224648 |
Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [H3K27ac ChIP-seq] |
|
| Relations |
| BioSample |
SAMN33141977 |
| SRA |
SRX19293584 |
