|
Status |
Public on Apr 01, 2021 |
Title |
ARID1A_CUTRUN_T3_rep2 |
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: 10nM T3 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 |
SAMN18244065 |
SRA |
SRX10307006 |