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Sample GSM5155227 Query DataSets for GSM5155227
Status Public on Apr 01, 2021
Title BRG1_CUTRUN_vehicle_rep1
Sample type SRA
 
Source name normal thyroid epithelial cell line Nthy-ORI
Organism Homo sapiens
Characteristics cell line: Nthy-ORI
cell type: normal thyroid epithelial cell
time: 6 hours
treatment: vehicle
data type: CUT&RUN
Treatment protocol Cells were treated with 10nM T3 or vehicle (NaOH) treatment for 6 or 24 hours.
Growth protocol Cells were hormone starved in phenol-red free culture media with charcoal stripped FBS for 24 hours, followed by the addition of 10nM T3 or vehicle (NaOH) treatment for 6 or 24 hours.
Extracted molecule genomic DNA
Extraction protocol nuclei from 500,000 cells were extracted and subjected to CUT&RUN protocol using the indicated antibody.
NEB Next Ultra II FS DNA Library Kit (CUT&RUN)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Data processing Library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.7
illumina adapters were removed with TrimGalore
trimmed reads were mapped to hg38 using bowtie2
peaks were called with MACS2
consensus peak sets were generated using IDR
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak file, consensus peaks dervied from two replicates
 
Submission date Mar 10, 2021
Last update date Apr 01, 2021
Contact name Frances Carr
E-mail(s) frances.carr@uvm.edu
Organization name University of Vermont
Department Pharmacology
Street address 149 Beaumont Ave, HSRF 340
City Burlington
State/province Vermont
ZIP/Postal code 05405
Country USA
 
Platform ID GPL18460
Series (2)
GSE168656 T3-Dependent Transcriptional Programming by TR-beta Requires SWI/SNF Chromatin Remodelers (CUT&RUN)
GSE168954 T3-Dependent Transcriptional Programming by TR-beta Requires SWI/SNF Chromatin Remodelers
Relations
BioSample SAMN18244072
SRA SRX10306999

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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