NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4987126 Query DataSets for GSM4987126
Status Public on Apr 13, 2021
Title FlatCoatedRetriever1 - PBMCs H3K4me1
Sample type SRA
 
Source name peripheral blood mononuclear cells
Organism Canis lupus familiaris
Characteristics cell type: peripheral blood mononuclear cells
breed: Flat Coated Retriever
antibody: H3K4me1
Growth protocol Fresh whole blood samples were collected in ACD tubes
Extracted molecule genomic DNA
Extraction protocol PBMCs were isolated with FICOLL-paque plus. SimpleChIP® Plus Enzymatic Chromatin IP kit, digested chromatin was sonicated, and Abcam #ab8895 and #ab8580 antibodies were used.
ChIPseq libraries were constructed using Ovation UltralowSystem V2 1-96 with 15 cycles of PCR amplification. Final libraries were twice purified with Ampure XP PCR Purification Beads (Agencourt). Pooled libraries were run with MiSeq Nano kit version 2.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
 
Data processing Basecalling was performed with RTA 2.4.11
Reads were aligned with BWA-MEM and converted to BAM files using samtools 1.10
Peaks were called with MACS2 2.2.1
Genome_build: CanFam 3.1
Supplementary_files_format_and_content: peak text files
 
Submission date Dec 23, 2020
Last update date Apr 13, 2021
Contact name Alexander Christian Harris
E-mail(s) alex.harris@nih.gov
Phone 301-402-2016
Organization name National Institutes of Health
Department National Human Genome Research Institute
Lab Ostrander
Street address 50 South Drive
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL28490
Series (2)
GSE163779 Canine Blood ChIP-seq
GSE163784 Canine
Relations
BioSample SAMN17148374
SRA SRX9724957

Supplementary file Size Download File type/resource
GSM4987126_FCR1_H3K4me1_peaks.narrowPeak.gz 1.2 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.