From here you can freely download the data from ESCAPE database.
You can either download each table seperately or download the entire database. The file formats available are either flat text file or sql.

Interactions from Chip-seq/chip studies

Description:
The protein/DNA interactions table is extracted from ChIP-X studies. We collect interactions from supplementary Excel tables from ChIP-chip and ChIP-seq experiments. These interactions are also available in ChEA developed by the Ma'ayan laboratory . Altogether, the current version of ESCAPE includes 206,521 protein-DNA binding interactions in proximity to coding regions covering 48 ESC-relevant transcription factors and chromatin modifiers.

Files:
chip_x.txt.zip
chip_x.sql.zip

Interactions from logof followed by microarrays

Description:
Protein-mRNA regulatory interactions extracted from studies of loss-of-function or gain-of-function followed by mRNA microarray profiling. Targets genes are identified as significantly changing in perturbation experiments in which a pluripotency protein under investigation is either knocked down or over-expressed. We manually collected protein regulatory targets from Supplementary Tables in relevant articles when it was available. Otherwise we processed the raw data deposited in GEO database to identify differentially expressed genes. Criteria for targets filtering is specified in the 'comments' column of the table. The table contains 153,920 interactions, describing the mRNA-level regulatory information of for 16 ESC-regulatory proteins from loss-of-function and 54 from gain-of-function studies.

Files:
logof.txt.zip
logof.sql.zip

Protein protein interactions

Description:
Protein-protein interactions (PPIs) are extracted from 5 high-throughput proteomics and 76 low-throughput protein-protein interaction studies. We collected PPIs from high-throughput affinity immunoprecipitation followed by mass-spectrometry proteomics using key TF regulators as baits. The table also contains interactions from low-throughput studies. Currently this table contains 1,037 PPI interactions.

Files:
ppi.txt.zip
ppi.sql.zip

miRNA target interactions

Description:
miRNA-predicted targets are consolidated from several publicly available databases: TarBase, TargetScan, miRander and miRBase. Except TarBase which exclusively contains experimentally validated targets, the other three databases mostly contain targets predicted using computational algorithms.

Files:
miRNAtargets.txt.zip
miRNAtargets.sql.zip

Putative pluripotency genes determined by RNAi screens

Description:
Potential pluripotency associated genes from multiple genome-wide RNAi screens studies.

Files:
RNAihits.txt.zip
RNAihits.sql.zip

Undifferentiated and differentiating ESC specific proteins

Description:
Lists of ESC and diffferentiating ESC-specific proteins. We collected 19,801 ESC and diffferentiating ESC-specific proteins from proteomics.

Files:
proteomicsESC.txt.zip
proteomicsESC.sql.zip

Histone modification determined by Chip-seq/chip

Description:
Histone modification profiles of genes in ESCs, NPCs and MEFs etc. were converted to gene lists. We compiled the histone modification table by integrating results from ten studies covering a total of 107 histone modification markers in ESCs, iPSCs, Mouse Embryonic Fibroblasts (MEFs), Neural Progenitor Cells (NPCs) and whole brain cells.

Files:
histoneModification.txt.zip
histoneModification.sql.zip

Undifferentiated and differentiating ESC specific phosphoproteins from phosphoproteomics

Description:
ESC and diffferentiating ESC-specific phosphoproteins with specified phosphosites. We collected 8,323 ESC and diffferentiating ESC-specific phosphoproteins with specified phosphosites from phosphoproteomics studies

Files:
phosphoproteinhits.txt.zip
phosphoproteinhits.sql.zip

Genome-wide mRNA expression profiles dataset summary

Description:
List of all time-course gene expression profiles available under different conditions.

Files:
expr_Summary.txt.zip
expr_Summary.sql.zip

miRNA expression

Description:
miRNA expression in mouse ESCs, MEFs and iPSCs.

Files:
miRNA_MEF_MES_iPS_signal.txt.zip
miRNA_MEF_MES_iPS_signal.sql.zip

Time course expression from J1 #1

Description:
Time-course gene expression of J1 ESCs under undirected differentiation using Affymatrix MOE430A array.

Files:
J1_ES_EB_MOE430A.txt.zip
J1_ES_EB_MOE430A.sql.zip

Time course expression from J1 #2

Description:
Time-course gene expression of J1 ESCs under undirected differentiation using Affymatrix MOE430B array.

Files:
J1_ES_EB_MOE430B.txt.zip
J1_ES_EB_MOE430B.sql.zip

Time course expression from R1 #1

Description:
Time-course gene expression of R1 ESCs under undirected differentiation using Affymatrix MOE430A array.

Files:
R1_ES_EB_MOE430A.txt.zip
R1_ES_EB_MOE430A.sql.zip

Time course expression from R1 #2

Description:
Time-course gene expression of J1 ESCs under undirected differentiation using Affymatrix MOE430B array.

Files:
R1_ES_EB_MOE430B.txt.zip
R1_ES_EB_MOE430B.sql.zip

Time course expression from V6.5 #1

Description:
Time-course gene expression of V6_5 ESCs under undirected differentiation using Affymatrix MOE430A array.

Files:
V6_5_ES_EB_MOE430A.txt.zip
V6_5_ES_EB_MOE430A.sql.zip

Time course expression from V6.5 #2

Description:
Time-course gene expression of V6_5 ESCs under undirected differentiation using Affymatrix MOE430B array.

Files:
V6_5_ES_EB_MOE430B.txt.zip
V6_5_ES_EB_MOE430B.sql.zip

Time-course expression of shRNAi #1

Description:
shRNAi induced differentiation time courses in mouse ESCs on Affymetrix MOE430A array

Files:
Ivanova_shRNAi_MOE430A.txt.zip
Ivanova_shRNAi_MOE430A.sql.zip

Time-course expression of shRNAi #2

Description:
shRNAi induced differentiation time courses in mouse ESCs on Affymetrix MOE430B array

Files:
Ivanova_shRNAi_MOE430B.txt.zip
Ivanova_shRNAi_MOE430B.sql.zip

All expression data

Description:
All the time-course gene expression of the database. This comprise tables expr_Summary, J1_ES_EB_MOE430A , J1_ES_EB_MOE430B, V6_5_ES_EB_MOE430A , V6_5_ES_EB_MOE430B, R1_ES_EB_MOE430A, R1_ES_EB_MOE430B and miRNA_MEF_MES_iPS_signal.

Files:
All_expr.txt.zip
All_expr.sql.zip

ESCAPE

Description:
The entire ESCAPE database.

Files:
StemCells.txt.zip
StemCells.sql.zip