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Table 1 24 ATAC-seq or ATAC-seq/RNA-seq paired datasets used in this study

From: SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors

Name

Tasks

Description

RNA-seq

ATAC-seq

# cond

Refs

Ascl1

4,6

Ascl-1-induced mouse neural reprogramming

GSE43916

GSE101397

4

[25, 59,60,61]

Duren

1,2,3,4

Retinoic acid (RA)-induced mESC differentiation

GSE136312

GSE136312

6

[35, 62]

Perrin

1,2,3,4

Human adipocyte differentiation

GSE178795

GSE178794

5

[51, 63, 64]

Ramirez

(macrophage, monocyte derived, monocyte)

1,2,3,4

Human myeloid differentiation

GSE79044

GSE79019

30

[46, 65, 66]

Liu

1,2,3,4

Human cardiac differentiation

GSE85331

GSE85330

16

[44, 67, 68]

Markov

1,2,3,4

Human early iPSC reprogramming

GSE121052

GSE120992

10

[45, 69, 70]

Schwarz

1,2,3,4

Human iPSC reprogramming

GSE106836

GSE106834

7

[41, 71, 72]

Liu2

1,2,3,4

Human-induced trophoblast stem cell reprogramming

GSE150616

GSE150590

3

[43, 73, 74]

Melendez

1,2,3,4

Human dopaminergic neuron differentiation

GSE153005

GSE153005

4

[75, 76]

Benchetrit

1,2,3,4

Mouse blastocyst cell reprogramming

GSE98124

GSE98124

7

[40, 77]

Wu

1,2,3,4

Human somatic cell reprogramming

GSE147679

GSE147678

11

[39, 78, 79]

Yagi

1,2,3,4

Mouse nature myocytes and myogenic stem cell trans-differentiation

GSE169488

GSE169488

15

[38, 80]

Knaupp

1,2,3,4

Human iPSC reprogramming

GSE101905

GSE101905

9

[37, 81]

Li

1,2,3,4,6

Mouse iPSC reprogramming

GSE93027

GSE93026

14

[36, 82, 83]

Zenere

1,2,3,4

T-help type 1 (Th1) differentiation

E-MTAB-7775

E-MTAB-10423

E-MTAB-10444

13

[34, 84,85,86]

Maza

1,2,3

Somatic cell trans-differentiation

 

GSE67298

4

[47, 87]

Qu

1,2,3

Primary human T cells

 

GSE60682

29

[53, 88]

Denny

1,2,3

Primary tumors and metastases

 

GSE81255

31

[48, 89]

Zviran

1,2,3

Somatic cell reprogramming

 

GSE103821

16

[49, 90]

Corces

1,2,3

Hematopoietic and leukemic cells

 

GSE74912

130

[50, 91]

GM12878

5

Human LCL (GM12878)

 

GSE47753

1

[13, 92]

Tang

1,2,3

MCF-7 cells with retinoic acid and/or TGF-beta

 

GSE152749

4

[42, 93]

K562

5

Human K562 cells

 

GSE170378

1

[58, 94]

Etv2

5,6

Etv2-induced reprogramming and differentiation

 

GSE168636

17

[95, 96]

Buenrostro

 

Human hematopoietic differentiation

 

GSE96771

13

[33, 97]