|
Status |
Public on Jun 07, 2023 |
Title |
Rax-GFP ESCs, H3K27ac antagonist Rep 1 |
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
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|
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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 |
SAMN33141978 |
SRA |
SRX19293583 |