Supplementary Figure Genes with high expression divergence between selected cells and tissues, as measured by Phylogenetic anova


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NameSupplementary Figure Genes with high expression divergence between selected cells and tissues, as measured by Phylogenetic anova
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Gene expression signatures of human cell and tissue longevity
Inge Seim1, Siming Ma1, and Vadim N. Gladyshev1*

1 Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
* Corresponding author: Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, New Research Building, Room 435, 77 Avenue Louis Pasteur, Boston, MA 02115 USA. Phone: (617) 525-5122. E-mail: vgladyshev@rics.bwh.harvard.edu
Supplementary Information

SUPPLEMENTARY FIGURE 1



Supplementary Figure 1. RNA-seq quality assessment.
(A) Boxplot of quantile-normalized RNA-seq counts.
(B) Boxplot of correlation coefficients (Pearson's r) between biological replicates. A correlation coefficient between 0.9 and 1.0 indicate samples that can be considered highly correlated.


SUPPLEMENTARY FIGURE 2



Supplementary Figure 2. Genes with high expression divergence between selected cells and tissues, as measured by Phylogenetic ANOVA.
(A) Heart.
(B) Thyroid (gland).
(C) Hematopoietic; spleen, bone marrow and monocyte.
Phylogenetic ANOVA was performed by comparing the highlighted ‘lineage’ to all other samples, with a phylogeny-adjusted P-value ≤ 0.01 considered significant. Scaled log2 transformed normalized read counts (denoted as the row Z-score) are plotted in blue–red color, with red indicating high expression and blue indicating low expression.



Supplementary Figure 3. The complex SNRPN-SNURF locus positively correlates with cellular turnover.
A bicistronic SNRPN-SNURF mRNA gives rise to the proteins SNRPN (small nuclear ribonucleoprotein polypeptide N; SmN) and SNURF (SNRPN upstream reading frame). SNRPN and SNURF coding exon sequences and scatterplot points are shown as blue and red, respectively. Error bars indicate standard error of the mean. FDR P denotes false discovery rate P-value.




Supplementary Figure 4. The ‘guardian of the genome’, p53 (TP53), negatively correlates with cellular turnover.
Error bars indicate standard error of the mean. FDR P denotes false discovery rate P-value.

Supplementary Table 1. Detailed information of RNA-seq samples.
Ostensible germ layer origins were derived from Vickaryous and Hall1. NA: Not Available; HPA: Human Protein Atlas.


Tissue/cell type

Germ layer

Estimated

turnover (days)

Literature

source(s)

Number

of samples

Mean age of human donors (years)

Adipose tissue

mesoderm

2,448

2-4

7

63

Adrenal gland

ectoderm

455

5

6

54

Bone marrow

mesoderm

3.2

6

8

47

(CD14+) monocyte

mesoderm

2




6

NA

Colon

endoderm

3.5




8

65

Endometrium

mesoderm

13




9

55

Esophagus

endoderm

10

13

6

61

Heart muscle

mesoderm

25,300




9

53

Keratinocyte (skin epidermis)

ectoderm

64

16

5

NA

Kidney

mesoderm

270

5

4

57

Liver

endoderm

327

17

5

63

Lung

endoderm

200

18

8

69

Neuron (neocortex)

ectoderm

32,850




4

66

Osteoblast (bone)

mesoderm

8.3




2

NA

Rectum

endoderm

3.5




4

70

Salivary gland

ectoderm

60

23

6

50

Skeletal muscle

mesoderm

5,510

19

32

HPA(6): NA

24(26): 27

Smooth muscle

mesoderm

67.5




3

54

Spleen

mesoderm

7.8

27

5

29

Thyroid gland

endoderm

3,180

 28


9

45

Urinary bladder

endoderm

49

29


6

77



Supplementary Table 2. Summary of RNA-sequencing data.
Aligned paired-reads in TopHat, Pearson coefficients of biological replicates and literature sources of the samples are listed.

sample name

sample type

aligned paired reads

Pearson correlation of biological replicate

reference(s)

ERR315332

adipose tissue

13,679,690

1.00




ERR315342

adipose tissue

15,718,516

0.97




ERR315343

adipose tissue

2,138,967

0.95




ERR315378

adipose tissue

7,371,560

0.97




ERR315431

adipose tissue

2,508,174

0.96




ERR579122

adipose tissue

31,982,215

0.93




ERR579146

adipose tissue

38,163,297

0.93




ERR315335

adrenal gland

4,699,590

1.00




ERR315385

adrenal gland

5,238,333

0.97




ERR315392

adrenal gland

4,501,896

0.97




ERR315417

adrenal gland

7,066,673

0.97




ERR315450

adrenal gland

6,093,356

0.98




ERR315452

adrenal gland

6,346,397

0.99




ERR315333

bone marrow

13,209,582

1.00




ERR315395

bone marrow

13,025,511

0.99




ERR315396

bone marrow

12,871,598

0.97




ERR315404

bone marrow

13,741,727

0.96




ERR315406

bone marrow

13,906,375

0.96




ERR315425

bone marrow

11,649,721

0.95




ERR315469

bone marrow

11,879,854

0.95




ERR315486

bone marrow

12,707,596

0.97




ERR315348

colon

9,856,467

1.00




ERR315357

colon

28,063,977

0.96




ERR315400

colon

15,405,148

0.97




ERR315403

colon

3,977,193

0.96




ERR315462

colon

8,956,738

0.96




ERR315484

colon

19,398,532

0.98




ERR579129

colon

35,017,647

0.95




ERR579148

colon

43,462,253

0.95




ERR315361

endometrium

6,042,492

1.00




ERR315368

endometrium

5,465,669

0.95




ERR315386

endometrium

4,179,293

0.95




ERR315433

endometrium

5,475,801

0.95




ERR315438

endometrium

4,185,955

0.95




ERR315490

endometrium

6,062,592

0.99




ERR315495

endometrium

10,811,413

0.99




ERR579123

endometrium

33,679,045

0.96




ERR579138

endometrium

35,419,710

0.95




ENCSR000CPL-keratinocyte-5-1

epidermis (skin)

112,816,849

1.00

32

ENCSR000EYT-keratinocyte-1-1

epidermis (skin)

12,974,589

0.93

32

ENCSR000EYT-keratinocyte-1-2

epidermis (skin)

12,299,960

0.93

32

ENCSR000EYT-keratinocyte-1-3

epidermis (skin)

8,015,234

0.93

32

ENCSR000EYT-keratinocyte-2-1

epidermis (skin)

26,677,926

0.99

32

ERR315362

esophagus

9,306,826

1.00




ERR315398

esophagus

11,071,355

0.98




ERR315411

esophagus

9,884,140

0.99




ERR315434

esophagus

7,662,469

0.95




ERR315472

esophagus

10,432,584

0.98




ERR315489

esophagus

8,142,589

0.95




ERR315328

heart muscle

10,360,590

1.00




ERR315331

heart muscle

11,482,236

0.96




ERR315356

heart muscle

13,626,629

0.95




ERR315367

heart muscle

11,643,965

0.96




ERR315384

heart muscle

13,654,400

0.97




ERR315389

heart muscle

6,095,482

0.98




ERR315413

heart muscle

13,626,741

0.97




ERR315430

heart muscle

13,358,866

0.95




ERR315435

heart muscle

6,076,168

0.98




ERR315383

kidney

11,022,817

1.00




ERR315443

kidney

14,801,166

0.98




ERR315468

kidney

7,389,319

0.97




ERR315494

kidney

10,068,226

0.98




ERR315327

liver

4,709,463

1.00




ERR315394

liver

4,685,285

0.97




ERR315414

liver

13,756,011

0.96




ERR315451

liver

11,253,297

0.96




ERR315463

liver

11,429,118

0.96




ERR315326

lung

4,967,444

1.00




ERR315341

lung

20,476,728

0.97




ERR315346

lung

17,083,332

0.97




ERR315353

lung

5,866,789

0.96




ERR315424

lung

3,717,500

0.98




ERR315439

lung

3,229,871

0.97




ERR315444

lung

3,288,873

0.97




ERR315487

lung

7,892,387

0.99




ENCSR000CUC-CD14-positive-monocyte-1-1

monocyte

16,998,339

1.00

32

ENCSR000CUC-CD14-positive-monocyte-1-2

monocyte

17,581,190

0.99

32

ENCSR000CUC-CD14-positive-monocyte-1-3

monocyte

17,323,513

0.99

32

ENCSR000CUC-CD14-positive-monocyte-2-1

monocyte

17,329,200

0.97

32

ENCSR000CUC-CD14-positive-monocyte-2-2

monocyte

17,810,277

0.97

32

ENCSR000CUC-CD14-positive-monocyte-2-3

monocyte

17,888,947

0.97

32

SRR1206036

neuron

28,582,237

1.00

20

SRR1206037

neuron

31,047,471

0.97

20

SRR1206038

neuron

36,924,399

0.92

20

SRR1206039

neuron

24,776,033

0.95

20

ENCSR000CUF-osteoblast-1-1

osteoblast (bone)

156,890,689

1.00

32

ENCSR000CUF-osteoblast-2-1

osteoblast (bone)

151,690,295

0.97

32

ERR579127

rectum

33,859,853

1.00




ERR579140

rectum

37,902,377

0.97




ERR579147

rectum

32,008,071

0.97




ERR579151

rectum

38,609,843

0.97




ERR315325

salivary gland

10,435,059

1.00




ERR315382

salivary gland

10,607,164

0.99




ERR315418

salivary gland

7,043,950

0.96




ERR315420

salivary gland

10,852,477

0.97




ERR315449

salivary gland

6,970,847

0.96




ERR315459

salivary gland

11,039,613

0.97




ERR579130

skeletal muscle

8,613,622

1.00




ERR579141

skeletal muscle

8,836,311

0.96




ERR579142

skeletal muscle

8,155,622

0.95




ERR579143

skeletal muscle

4,033,724

0.94




ERR579149

skeletal muscle

9,477,219

0.95




ERR579152

skeletal muscle

7,514,321

0.96




SRR1424731

skeletal muscle

10,383,681

0.96

24

SRR1424732

skeletal muscle

11,102,989

0.96

24

SRR1424733

skeletal muscle

19,407,539

0.96

24

SRR1424734

skeletal muscle

13,419,304

0.95

24

SRR1424735

skeletal muscle

21,755,858

0.96

24

SRR1424736

skeletal muscle

12,898,986

0.96

24

SRR1424737

skeletal muscle

12,333,249

0.96

24

SRR1424738

skeletal muscle

9,226,277

0.96

24

SRR1424739

skeletal muscle

19,396,953

0.97

24

SRR1424740

skeletal muscle

11,778,037

0.99

24

SRR1424741

skeletal muscle

6,109,444

0.96

24

SRR1424742

skeletal muscle

15,341,805

0.96

24

SRR1424743

skeletal muscle

10,867,355

0.96

24

SRR1424744

skeletal muscle

14,307,991

0.96

24

SRR1424745

skeletal muscle

10,750,775

0.96

24

SRR1424746

skeletal muscle

9,331,743

0.96

24

SRR1424747

skeletal muscle

9,943,023

0.96

24

SRR1424748

skeletal muscle

11,669,684

0.96

24

SRR1424749

skeletal muscle

18,352,002

0.96

24

SRR1424750

skeletal muscle

13,895,243

0.94

24

SRR1424751

skeletal muscle

5,661,423

0.95

24

SRR1424752

skeletal muscle

11,773,405

0.96

24

SRR1424753

skeletal muscle

17,814,068

0.96

24

SRR1424754

skeletal muscle

20,423,449

0.96

24

SRR1424755

skeletal muscle

5,618,474

0.95

24

SRR1424756

skeletal muscle

4,739,452

0.94

24

ERR579125

smooth muscle

31,491,954

1.00




ERR579131

smooth muscle

28,510,726

0.93




ERR579153

smooth muscle

32,073,223

0.94




ERR315338

spleen

18,167,169

1.00




ERR315405

spleen

7,388,796

0.98




ERR315416

spleen

7,191,016

0.98




ERR315448

spleen

18,877,858

0.99




ERR315473

spleen

16,191,328

0.99




ERR315337

thyroid gland

18,756,280

1.00




ERR315358

thyroid gland

13,535,594

0.96




ERR315363

thyroid gland

9,754,177

0.97




ERR315397

thyroid gland

11,026,863

0.97




ERR315412

thyroid gland

18,856,626

1.00




ERR315422

thyroid gland

13,440,117

0.96




ERR315428

thyroid gland

9,719,953

0.97




ERR315483

thyroid gland

7,871,271

0.97




ERR315491

thyroid gland

7,836,954

0.97




ERR315334

urinary bladder

3,896,681

1.00




ERR315355

urinary bladder

12,344,532

0.96




ERR315370

urinary bladder

3,319,098

0.95




ERR315421

urinary bladder

3,123,367

0.95




ERR315447

urinary bladder

11,582,834

0.99




ERR315453

urinary bladder

3,677,518

0.99



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