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Sample GSM6133737 Query DataSets for GSM6133737
Status Public on Oct 20, 2023
Title leucogenys_gibbon_M_input_rep2
Sample type SRA
 
Source name LCL
Organism Nomascus leucogenys
Characteristics tissue: LCL
seq_assay: ChIP
common_name: Northern white-cheecked gibbon
Sex: M
chip antibody: INPUT
Extracted molecule genomic DNA
Extraction protocol ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
deeptools was used to calculate RPKM normalized signal of each epigenetic mark across the genome and at TAD boundaries
ChromHMM was used to annotate chromatin states using the mouse alignments
Assembly: mm10, mPah1, mCar1, nomLeu4, hMol2
Supplementary files format and content: bigWig; bed
Supplementary files format and content: *-CTCF-peaks-combined-merge200bp-sorted.bed: bed files contain all CTCF peaks unionized between one male and one female replicate, and merged within 200bp.
 
Submission date May 11, 2022
Last update date Oct 30, 2023
Contact name Mariam Okhovat
Organization name Oregon Health and Science University
Department Medicine
Street address 3030 S Moody Ave.
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
 
Platform ID GPL27430
Series (1)
GSE197926 TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function
Relations
BioSample SAMN28196631
SRA SRX15239186

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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