Additional File 1, Table S1 - BioMed Central

Additional File 1, Table S1 Accession number Cell Line Pair A P63324 P14869 P18687 P47738 P4773 O08782 P07150 P04083 P55260 P00173 P29692 Q9D8N Q13347

Gene Name

Protein Name

RPS12 RPLP0 HSPD1 ALDH2 ALDH2 AKR1B8 ANXA1 ANXA1 ANXA4 CYB5A EEF1D EEF1G EIF3I

40S ribosomal protein S12 60S acidic ribosomal protein P0 60 kDa heat shock protein, mitochondrial Aldehyde dehydrogenase, mitochondrial Aldehyde dehydrogenase, mitochondrial Aldose reductase-related protein 2 Annexin A1 Annexin A1 Annexin A4 Cytochrome b5 Elongation factor 1-delta Elongation factor 1-gamma Eukaryotic translation initiation factor 3 subunit I Glucose-6-phosphate 1-dehydrogenase Glutathione peroxidase 1 Heat shock cognate 71 kDa protein Heat shock cognate 71 kDa protein Endoplasmin Endoplasmin Heterogeneous nuclear ribonucleoprotein A/B Hypoxia up-regulated protein 1 Inosine-5'-monophosphate dehydrogenase 2 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial Isopentenyl-diphosphate Delta-isomerase 1 Leucine carboxyl methyltransferase 1 Lysosomal alpha-glucosidase Major vault protein Mitochondrial import inner membrane translocase subunit TIM50 Neighbor of COX4 Nuclear migration protein nudC Peroxiredoxin-2

O55044 P11352 P19378 P19378 P14625 P14625 Q99729 Q60432 P12269 Q9D6R2

G6PD GPX1 HSPA8 HSPA8 HSP90B1 HSP90B1 HNRNPAB HYOU1 IMPDH2 IDH3A

Q13907 Q9UIC8 P70699 Q9EQK5 Q9D880

IDI1 LCMT1 GAA MVP TIMM50

O70378 Q63525 Q8K3U7

COX4NB NUDC PRDX2

Ratio SQp D3 v NSQp D3

Ratio SQp D7 v NSQp D7

Ratio SQp D10 v NSQp D10

1.39 14.31 1.8 1.42 2.12 1.82 -2.67 -9.79 -1.32 -5.91 2.23 2.34 1.44

2.15 7.5 3.73 1.53 2.06 1.7 -1.37 -9.49 -1.42 -5.21 2.1 2.22 1.93

2.27 4.56 2.87 1.73 1.94 1.2 -3.32 -12.34 -1.67 -2.81 1.92 2.2 1.35

-1.79 1.32 1.5 1.42 3.69 -1.42 5.14 4.66 1.94 1.52

-1.78 2 1.94 1.69 2.19 -1.51 5.1 3.79 -1.15 2.05

-2.38 2.29 1.84 1.68 1.63 -10.55 2.46 2.46 -1.93 1.94

-5.24 3.5 5.41 2.04 -3.77

-2.43 1.75 6.62 2.36 -2.12

-1.97 1.54 5.79 3.18 -1.77

1.8 -9.26 1.56

2.64 -7.83 2.05

2.31 -7.45 2.33

Q9DBJ1 P61759 P67779 P60901 P70195 Q9R1P1 P05964 P26043 P34022 Q9Y265 Q9Y230 Q64303 Q9NR45 O54981 P11984 P11984 P50990 Q8VI73 P46462

PGAM1 VBP1 PHB PSMA6 PSMB7 PSMB3 S100A6 RDX1 RANBP1 RUVBL1 RUVBL2 PAK2 NANS STIP1 TCP1 TCP1 CCT8 TALDO1 VCP

P46462

VCP

P13693 P48500 Q9BQE3 P68371 P69893 P31254 P62815

TPT1 TPI1 TUBA1C TUBB2C TUBB5 UBEIAY ATP6V1B2

Cell Line Pair B 38982 P38982 P18687 P55262 Q9WTP6 P47738 O08782 P06733 P07150

RPSA RPSA HSPD1 ADK AK2 ALDH2 AKR1B8 ENO1 ANXA1

Phosphoglycerate mutase 1 Prefoldin subunit 3 Prohibitin Proteasome subunit alpha type-6 Proteasome subunit beta type 7 Proteasome subunit beta type-3 Protein S100-A6 Radixin Ran-specific GTPase-activating protein RuvB-like 1 RuvB-like 2 Serine/threonine-protein kinase PAK 2 Sialic acid synthase Stress-induced-phosphoprotein 1 T-complex protein 1 subunit alpha T-complex protein 1 subunit alpha T-complex protein 1 subunit theta Transaldolase Transitional endoplasmic reticulum ATPase (Valosin-containing protein) Transitional endoplasmic reticulum ATPase (Valosin-containing protein) Translationally-controlled tumor protein Triosephosphate isomerase Tubulin alpha-1C chain Tubulin beta-2C chain Tubulin beta-5 chain Ubiquitin-like modifier-activating enzyme 1 Y V-type proton ATPase subunit B, brain isoform

1.66 12.26 -2.28 2.16 1.78 -1.16 -1.6 1.77 2.99 2.2 3.31 -1.2 -3.08 1.65 3.64 -2.94 3.37 15.04 -2.87

4.85 6.51 -1.52 4.38 2.03 -1.1 -1.08 1.31 5.18 3.56 2.52 -1.83 -2.02 2.11 3.81 -1.7 5.04 13.19 -4.72

4.23 2.25 -1.64 3.53 1.45 -2.86 1.87 -1.04 7.6 2.83 2.82 -2.2 -1.94 1.73 3.08 -2.01 2.91 9.49 -4.23

-4.78

-8.77

-11.12

1.55 -1.88 1.04 1.24 6.7 -5.83 -1.19

2.53 -1.54 -1.36 1.44 6.63 -5.33 -1.59

2.24 -1.69 -1.84 2.5 4.58 -5.89 -3.45

40S ribosomal protein SA 40S ribosomal protein SA 60 kDa heat shock protein, mitochondrial Adenosine kinase (AK) Adenylate kinase 2, mitochondrial Aldehyde dehydrogenase, mitochondrial Aldose reductase-related protein 2 Alpha-enolase Annexin A1

1.25 1.16 1.21 1.25 1.32 -1.23 1.85 -1.25 -1.48

1.18 1.12 1.11 1.15 1.28 -1.25 1.5 -1.21 -1.43

1.49 1.45 1.42 1.41 1.38 -1.06 1.43 1.2 -1.49

P97429 P48036 P37397 P23528 Q68FS4 O08651 Q62651

ANXA4 ANXA5 CNN3 CFL1 LAP3 PHGDH ECH1

Q80UW8

POLR2E

P29692 P09445 Q9CZR8 Q13347

EEF1D EEF2 TSFM EIF3I

Q9WUK2 P48538 O55044 P48508 Q60631 P19378 P14625 Q13907 Q4G075 Q4G075 Q63525 Q9DBJ1 P27773 Q8R4U2 Q64311 Q8K183 Q8WUD1 P47968 Q9Y265 Q9Y230 Q64303 P08228 P48500 P48500 Q6P7B0

EIF4H LGALS1 G6PD GCLM GRB2 HSPA8 HSP90B1 IDI1 SERPINB1A SERPINB1A NUDC PGAM1 PDIA3 P4HB NTAN1 PDXK RAB2B RPIA RUVBL1 RUVBL2 PAK2 SOD1 TPI1 TPI1 WARS

Annexin A4 Annexin A5 Calponin-3 Cofilin-1 Cytosol aminopeptidase D-3-phosphoglycerate dehydrogenase Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial DNA-directed RNA polymerases I, II, and III subunit RPABC1 Elongation factor 1-delta Elongation factor 2 Elongation factor Ts, mitochondrial Eukaryotic translation initiation factor 3 subunit I Eukaryotic translation initiation factor 4H Galectin-1 Glucose-6-phosphate 1-dehydrogenase Glutamate--cysteine ligase regulatory subunit Growth factor receptor-bound protein 2 Heat shock cognate 71 kDa protein Endoplasmin Isopentenyl-diphosphate Delta-isomerase 1 Leukocyte elastase inhibitor A Leukocyte elastase inhibitor A Nuclear migration protein nudC Phosphoglycerate mutase 1 Protein disulfide-isomerase A3 Protein disulfide-isomerase Protein N-terminal asparagine amidohydrolase Pyridoxal kinase Ras-related protein Rab-2B Ribose-5-phosphate isomerase RuvB-like 1 RuvB-like 2 Serine/threonine-protein kinase PAK 2 Superoxide dismutase [Cu-Zn] Triosephosphate isomerase Triosephosphate isomerase Tryptophanyl-tRNA synthetase, cytoplasmic

-1.47 1.29 -1.49 -1.88 1.3 -1.24 1.53

-1.48 1.28 -2.38 -2.72 1.26 -1.25 2.49

-1.43 1.34 -3.01 -5.86 1.27 -1.02 2.42

-1.87

-1.66

-1.63

-1.17 -1.06 1.22 1.2

-1.23 1.65 1.16 1.22

-1.29 1.91 1.4 1.53

-1.02 -1.58 -1.66 -1.06 -1.03 1.45 1.2 1.48 -1.5 -2.78 -1.09 1.35 -1.25 -1.58 -1.21 1.2 -1.56 1.4 1.44 -1.21 1.17 -1.39 2.19 2.34 -1.14

-1.35 -1.24 -1.89 -1.44 -1.03 1.33 1.23 1.57 -1.36 -1.91 -1.2 1.28 -1.3 -1.52 -1.09 1.22 -1.66 1.43 1.31 -1.32 1.16 -1.24 2.19 2.61 1.18

-1.52 -1.07 -1.72 -1.58 -1.36 1.5 1.28 1.58 -1.32 -1.49 -1.14 1.66 -1.19 -1.36 -1.26 1.53 -1.6 1.61 1.48 -1.31 1.28 -1.38 2.35 2.68 1.38

P48428 P61085 P61085 P61085

TBCA UBE2K UBE2K UBE2K

Tubulin-specific chaperone A Ubiquitin-conjugating enzyme E2 K Ubiquitin-conjugating enzyme E2 K Ubiquitin-conjugating enzyme E2 K

1.39 2 -1.15 1.21

1.32 1.8 -1.28 -1.4

1.4 1.84 -1.22 -1.78

Additional File 1, Table S2 A –Proteins differentially expressed only in the NSQp cell lines, when comparing Day 7&10 to Day 3 samples Accession number Cell Line Pair A P63324 P18687 Q13347 P14625. P42930 Q9DBJ1 P17918 P17918 P34022 Q9Y265 Q64303 O54981 P13693 Q9BQE3 Cell Line Pair B P38982 P18687 P07150 P23528 Q13347 O55044 Q13907 P38652 Q8K183 Q9Y230

Gene Name

Protein Name

Ratio D7&D10 v D3

RPS12 HSPD1 EIF3I HSP90B1 HSPB1 PGAM1 PCNA PCNA RANBP1 RUVBL1 PAK2 STIP1 TPT1 TUBA1C

40S ribosomal protein S12 60 kDa heat shock protein, mitochondrial Eukaryotic translation initiation factor 3 subunit I Endoplasmin Heat shock protein beta-1 Phosphoglycerate mutase 1 Proliferating cell nuclear antigen (PCNA) Proliferating cell nuclear antigen Ran-specific GTPase-activating protein RuvB-like 1 Serine/threonine-protein kinase PAK 2 Stress-induced-phosphoprotein 1 Translationally-controlled tumor protein Tubulin alpha-1C chain

-1.71 -1.9 -1.33 2.12 -1.48 -2.37 -1.63 -1.74 -1.96 -1.45 1.92 -1.42 -1.84 1.4

RPSA HSPD1 ANXA1 CFL1 EIF3I G6PD IDI1 PGM1 PDXK RUVBL2

40S ribosomal protein SA 60 kDa heat shock protein, mitochondrial Annexin A1 Cofilin-1 Eukaryotic translation initiation factor 3 subunit I Glucose-6-phosphate 1-dehydrogenase Isopentenyl-diphosphate Delta-isomerase 1 Phosphoglucomutase-1 Pyridoxal kinase (Pyridoxine kinase) RuvB-like 2

-1.61 -1.22 1.77 4.91 -1.28 1.24 -1.28 2.4 -1.28 1.28

Additional File 1, Table S2 B –Proteins differentially expressed only in the SQp cell lines, when comparing Day 7&10 to Day 3 samples Accession number Cell Line Pair A P14869 O08782 P37397 Q9D1A2 P11352 P13704 P12269 Q13907 Q9UIC8 Q9EQK5 O35987 Q62422 P61759 O14744 Cell Line Pair B O08782 P37397 Q62651

Gene Name

Protein Name

Ratio D7&D10 v D3

RPLP0 AKR1B8 CNN3 CNDP2 GPX1 HMGCS1 IMPDH2 IDI1 LCMT1 MVP NSFL1C OSTF1 VBP1 PRMT5

60S acidic ribosomal protein P0 Aldose reductase-related protein 2 Calponin-3 Cytosolic non-specific dipeptidase Glutathione peroxidase 1 Hydroxymethylglutaryl-CoA synthase, cytoplasmic Inosine-5'-monophosphate dehydrogenase 2 Isopentenyl-diphosphate Delta-isomerase 1 Leucine carboxyl methyltransferase 1 Major vault protein NSFL1 cofactor p47 Osteoclast-stimulating factor 1 Prefoldin subunit 3 Protein arginine N-methyltransferase 5

-2.34 -1.64 -4.85 1.86 1.32 -3.6 -2.6 1.58 -2.01 -1.62 -1.74 2.35 -2.24 -1.67

Aldose reductase-related protein 2 Calponin-3 Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial DNA-directed RNA polymerases I, II, and III subunit RPABC1 Eukaryotic translation initiation factor 4H Galectin-1 Long-chain specific acyl-CoA dehydrogenase, mitochondrial Tryptophanyl-tRNA synthetase, cytoplasmic

-1.41 -1.85 1.74

AKR1B8 CNN3 ECH1

Q80UW8

POLR2E

Q9WUK2 P48538 P15650

EIF4H LGALS1 ACADL

Q6P7B0

WARS

1.47 -1.38 1.61 1.41 1.66