Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Pluripotent stem cell

Cell type

iPSC derived chondrocytes

NA

NA

Sample

source_name

Human iPS-derived cells on day 2 of TT(-) protocol

cell type

Human iPS cells

tissue

Dermal fibroblasts

days after differentiation

2

antibody

None

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

For ATAC-seq, 50,000 cells were lysed to obtain nuclei in cold lysis buffer, and incubated in the Tn5 transposase reaction mix, as described previously (Buenrostro et al., 2013). For ChIP-seq, cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Protein-DNA complexes were purified with antibody. For ATAC-seq, DNA fragments were PCR-amplified using previously-designed barcoded primers, as described previously (Buenrostro et al., 2013).For ChIP-seq, libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer's instruction.

Sequencing Platform

instrument_model

Illumina HiSeq X Ten

hg38

Number of total reads

55437088

Reads aligned (%)

74.3

Duplicates removed (%)

45.3

Number of peaks

10977 (qval < 1E-05)

hg19

Number of total reads

55437088

Reads aligned (%)

74.1

Duplicates removed (%)

45.5

Number of peaks

10821 (qval < 1E-05)