Antigen

Antigen Class

TFs and others

Antigen

CTNNB1

Cell type

Cell type Class

Pluripotent stem cell

Cell type

hESC derived endodermal cells

NA

NA

Sample

source_name

Induced pluripotent stem cells

developmental stage

Day 2 endoderm progenitors

chip antibody

Invitrogen 71-2700

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For RNA-Seq experiments, Total RNA was extracted using the Nucleospin RNA Extraction kit.For ChIP-Seq experiments, after differentiation to the desired stage, cells were dual crosslinked in plate with 1.5mM EGS and 1% formaldehyde. The fixation was then quenched with 125mM glycine. Cells were then washed twice and scraped in ice-cold PBS and resuspended in sonication buffer.For ATAC-Seq experiments, 50,000 cells were collected following differentiation to the desired stage, and lysed in 50ul of ATAC-lysis buffer (10mM Tris-HCl, pH 7.4. 10mM NaCl, 3mM MgCl2, 0.1% NP-40) to obtain a crude nuclei prep For RNA-Seq experiments, 300ng of total RNA was poly-A selected and reverse transcribed using Illumina's TruSeq stranded mRNA library preparation kit (Illumina; 20020595). For ChIP-Seq experiments, DNA libraries were prepared using 1-5 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674) according to manufacturer's instructions. For ATAC-Seq, the eluted DNA was amplified in a reaction with 25ul NEBNext High-Fidelity 2x PCR Mastermix (NEB; M0541L) and custom 25um Nextera PCR Primers (Ad1_noMx universal primer, 0.5um Ad2.x indexing primer). PCR was performed as follows: 1 cycle of 72C for 5min, 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 1min. 5ul of the amplified DNA was then used to perform qPCR to determine the optimal number of additional cycles to prevent amplification saturation of DNA libraries. In all cases, either 4 or 5 additional cycles of PCR was performed at: 98C for 10s, 63C for 30s and 72C for 1 min. Double size selection of amplified libraries (0.5x – left sided, 1.8x – right sided) was performed using AMPure XP beads ChIP-Seq, RNA-Seq and ATAC-Seq

Sequencing Platform

instrument_model

Illumina NovaSeq 6000

hg38

Number of total reads

37071899

Reads aligned (%)

73.1

Duplicates removed (%)

10.9

Number of peaks

7504 (qval < 1E-05)

hg19

Number of total reads

37071899

Reads aligned (%)

72.4

Duplicates removed (%)

11.1

Number of peaks

7122 (qval < 1E-05)