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Sample GSM7029059 Query DataSets for GSM7029059
Status Public on Jun 07, 2023
Title Rax-GFP ESCs, H3K27ac control 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
 
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 SAMN33141980
SRA SRX19293581

Supplementary file Size Download File type/resource
GSM7029059_H3K27ac_control_Rep1.bigWig 307.4 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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