GSM3391514: ATAC-seq WT Day 7 - Replicate 1; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA
Attributes by original data submitter
Sample
source_name
Surface Ectoderm cells
cell line
H9
genotype/variation
wild-type
treatment
Day 7 of differentiation with RA/BMP4
cell type
Surface Ectoderm cells
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
After treatment with Accutase, 7x10^4 cells were washed with cold PBS and lysed using 0.1% NP40 in RSB buffer. Nuclei were then isolated by centrifugation. Nuclei pellets were Tn5 transposed using the DNA Sample Preparation Kit from Nextera®. Libraries were amplified for 9-15 total cycles using the Ad1 and Ad 2.1-2.16 barcodes. Libraries were purified using the Min-Elute columns (Qiagen) and eluted with 10 μL of buffer EB. Library DNA concentrations were determined with Bioanalyzer High-Sensitivity DNA analysis kit (Agilent). Paired-end libraries were sequenced initially on a MiSeq sequencer and analyzed using a custom script to determine the signal enrichment over background at TSSs over a 2 kb window. Only libraries that had enrichment scores above 6 were sequenced deeper in a NextSeq Illumina sequencer.