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SRX11955062: GSM5543598: fca_smallintestine_h3k27me3_rep1; Felis catus; ChIP-Seq
2 ILLUMINA (Illumina NovaSeq 6000) runs: 67.3M spots, 6.7G bases, 2.1Gb downloads

Submitted by: NCBI (GEO)
Study: Genome-wide mapping of regulatory regions in seven domestic cat tissues [ChIP-seq]
show Abstracthide Abstract
Histone modifications and CTCF mark the locations of genomic regulatory regions -- including promoters, enhancers, and insulators -- and have not been previously annotated for the domestic cat genome. Understanding where non-coding sequence variants fall in relation to regulatory regions is vital for determining their impact on gene function and their ability to cause disease. The addition of replicated feline ChIP-seq data from multiple tissues will aid in interpretation of non-coding variants, furthering characterization of genetic diseases and genetic test development. Overall design: Genomic DNA was extracted from seven tissues collected from adult male domestic shorthair cats (two biological replicates for each tissue), and ChIP-seq was performed with antibodies to three histone modifications (H3K27ac, H3K4me3, H3K27me3) and CTCF on all tissues. As a control, input DNA was sequenced for each tissue without the inclusion of an antibody. ENCODE quality metrics (NRF, PBC1, PBC2, NSC, and RSC) were calculated and included in the provided sample metadata.
Sample: fca_smallintestine_h3k27me3_rep1
SAMN21025041 • SRS9964802 • All experiments • All runs
Organism: Felis catus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Tissue samples were collected from adult male domestic shorthair cats (2 biological replicates). Tissues included: heart, liver, kidney, small intestine, testes, lung, and thyroid. No lesions were identified grossly in the collected tissues. Tissues were flash frozen within 30 minutes of euthanasia and stored at -80 C. All steps leading up to and including chromatin immunoprecipitation (ChIP) and ChIP qPCR were performed using the iDeal ChIP-seq Kit for Histones (Diagenode) per manufacturer guidelines. This included DNA sonication to 100-300 bp using a Bioruptor Pico (Diagenode) at 7 cycles of 30 seconds on and 30 seconds off. Library preparation for sequencing was performed with the NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext® Multiplex Oligos for Illumina (New England Biolabs) according to manufacturer guidelines. Sequencing was performed on a NovaSeq 6000 platform (Illumina) with a single-end 100 bp format.
Experiment attributes:
GEO Accession: GSM5543598
Links:
Runs: 2 runs, 67.3M spots, 6.7G bases, 2.1Gb
Run# of Spots# of BasesSizePublished
SRR1565808033,365,0793.3G1Gb2021-08-31
SRR1565808133,967,7453.4G1Gb2021-08-31

ID:
15873221

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