NM

NM(B6)

NM(ICR)

IVF(ICR)

ICSI(ICR)

A

B

C

D

E

F

G

H

I

J

1/8

1/4

1/2124

8

1/8

1/4

1/2124

8

1/8

1/4

1/2124

8

1/8

1/4

1/2124

8

1/8

1/4

1/2124

8

NM

NM(B6)

NM(ICR)

IVF(ICR)

ICSI(ICR)

2 4 6 8 10 12

0.0

0.5

1.0

1.5

2.0

2 4 6 8 10 12

0.0

0.5

1.0

1.5

2.0

2 4 6 8 10 12

0.0

0.5

1.0

1.5

2.0

2 4 6 8 10 12

0.0

0.5

1.0

1.5

2.0

2 4 6 8 10 12

0.0

0.5

1.0

1.5

2.0

STDE

V/M

EAN

FOLD

CHA

NGE

LOG(MEAM)

Supplmentary Figure 1

Gene expression profiles of mice conceived by natural mating, IVF and ICSI.

Gene expression profiles in neonatal liver from (A) pups produced by C57BL/6 (B6) mothers conceived by natural mating with DBA/2 males (D2) and undergoing continued pregnancy; NM, (B) pups born to a pseudo-pregnant C57BL/6 surrogate mother implanted with the embryos fertilized in vivo by natural mating of a C57BL/6 female with a DBA/2 male followed by flushing out; NM(B6), (C) pups born to a pseudo-pregnant ICR surrogate mother transplanted with the same embryo as (B); NM(ICR), (D) pups born to a pseudo-pregnant ICR surrogate mother transplanted with embryo fertilized in vitro; IVF(ICR), (E) pups born to a pseudo-pregnant ICR surrogate mother transplanted with embryo fertilized by ICSI; ICSI(ICR). The intensity of each signal from the DNA microarray was normalized by dividing it by the mean signal intensity of the samples of the NM(ICR). Genes which commonly exhibited a difference in their expression levels between NM plus NM(B6) and NM(ICR) are shaded in pale red. Genes that exhibited a difference in NM(B6) or ICSI alone are shaded in yellow or green, respectively. Gene expression dispersal in the neonatal liver from (F) pups produced by C57BL/6 (B6) mothers conceived by natural mating with DBA/2 males (D2) and continued pregnancy; NM, (G) pups born to a pseudo-pregnant C57BL/6 surrogate mother implanted with the embryos fertilized in vivo by natural mating of a C57BL/6 female with a DBA/2 male followed by flushing out; NM(B6), (H) pups born to a pseudo-pregnant ICR surrogate mother transplanted with the same embryo as (G); NM(ICR), (I) pups born to a pseudo-pregnant ICR surrogate mother transplanted with an embryo fertilized in vitro; IVF(ICR), (J) pups born to a pseudo-pregnant ICR surrogate mother transplanted with an embryo fertilized by intracy-toplasmic sperm injection; ICSI(ICR). The standard deviation of the signals divided by the mean signal (vertical axis) vs. the mean signal (horizontal axis) was plotted.

34.0 %

48.1 %

6.4 %3.4 %5.3 %

down-I

down-II

down-IIIdown-IV

up-I

up-II

up-IIIup-IVup-V

down-I

down-II

down-III

down-IV

up-I

up-II

up-III

up-IV

down-I

down-II

down-III

down-IV

up-I

up-IIup-III

up-IV

48.8 %

9.8 %

1.6 %

39.5 %

17.4 %

68.0 %

9.1 %

5.0 %

16.9 %

52.2 %

15.4 %

12.7 %

4.2 %

28.3 %

63.9 %

1.6 %

17.8 %

63.7 %

10.8 %5.9 %

IVF ICSI

0w

IVF ICSI

8w

IVF ICSI

0w

IVF ICSI

8w

IVF ICSI

0w

IVF ICSI

8w

IVF ICSI

0w

IVF ICSI

8w

IVF ICSI

0w

IVF ICSI

8w

IVF ICSI

0w

IVF ICSI

8w

Brain (BDF1) Liver (BDF1) Kidney(BDF1)

Supplmentary Figure 2

-

Gene expression changes according to growth.

Expression profiles of the genes which exhibited a more than two fold up down pattern in the brain, liver and kidney of IVF and ICSI neonates are represented as heat-maps. Genes are ordered according to the expres-sion changes at the neonatal and 8 week stage. Each expression pattern is boxed and named accordingly. At 8 week stage, gene expression changes observed at neonate were almost diminished.

7 8 9 10 11 12 13 14 15 16 17P2-01 Light/Dark transition

P2-02 Open-field test (1st)

P2-03 Open-field test (2nd)

P2-01 Home-cage activity test

P2-05 Passive avoidance test

P2-06 Tail-suspension test

P2-07 Hot-plate test

P2-08 Tail-flick test

Test No.Age (weeks)

Behavior/Neurology/Psychiatry

MethodsScreens

Supplmentary Figure 3

Beahviour-phenotyping platform.

In order to reduce the number of animals needed for the experiments, the same mice were used for multiple phenotyping assays. In order to eliminate the effects of prior handling, the test platform was constructed with the same order of multifaceted behavioral tests. Proce-dures of the behavioral tests are available on our home page (http://www.brc.riken.go.jp/lab/bpmp/SOPs/index_mc.html).

fertilization foster mother litter sizeICSI ICR 9, 10IVF ICR 9, 11natural mating and flush ICR 9, 9natural mating and flush B6 9, 10natural mating B6 (true mother) 10, 12

Supplmentary Table 1Litter size of the mice produced by ICSI, IVF and natural mating.

gene name fold change description gene name fold change descriptionIncreased in liver Decreased in liver2810403A07Rik 5.12 mRNA for mKIAA0907 protein Rag1 0.18 recombination activating gene 1Rpl22l1 4.84 similar to 60S ribosomal protein L22 4930573I19Rik 0.22 Trp-Asp repeat (WD-repeat) structure containing proteinItgae 4.34 integrin, alpha E, epithelial-associated Stau1 0.22 Arginine-rich region containing protein8030488J09Rik 4.23

15 days embryo male testis cDNA, RIKEN full-lengthenriched library, clone:8030488J09 product 5930430L01Rik 0.24

B16 F10Y cells cDNA, RIKEN full-length enrichedlibrary, clone:G370004A16 product

Far1 3.63 fatty acyl CoA reductase 1 Kif1b 0.24 kinesin family member 1BPrss35 3.31 protease, serine, 35 (Prss35) Cdk2 0.25 cyclin-dependent kinase 2Pnpla8 3.24 patatin-like phospholipase domain containing 8 Sfrs15 0.25 C-terminal domain-binding protein rA4 homologDld 3.24 dihydrolipoamide dehydrogenase Xpo4 0.26 mRNA for mKIAA1721 proteinNAP030342-1 3.24 Unknown Csad 0.26

0 day neonate lung cDNA, RIKEN full-length enrichedlibrary, clone:E030032L18 product

A_51_P295858 3.09 Unknown Galm 0.27 weakly similar to IBD1 PROTEINDynlt3 2.95 dynein light chain Tctex-type 3 AK038463 0.28

adult male hypothalamus cDNA, RIKEN full-lengthenriched library, clone:A230016A06 product

LOC237412 2.94 similar to RIKEN cDNA 3000002G13 (LOC237412) AK043928 0.2810 days neonate cortex cDNA, RIKEN full-length enrichedlibrary, clone:A830054A06 product

Mapk8 2.92 mitogen activated protein kinase 8 AK034047 0.30adult male diencephalon cDNA, RIKEN full-lengthenriched library, clone:9330151G05 product

AW549877 2.85 expressed sequence AW549877 AK054546 0.302 days pregnant adult female ovary cDNA, RIKEN full-length enriched library, clone:E330039N10

Arl6ip2 2.80 10 days neonate cortex cDNA Rufy3 0.30adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone:B230215E15 product

Ddx3x 2.79DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked AK032144 0.30 surfactant associated protein B

Dars 2.73 aspartyl-tRNA synthetase C130083B21Rik 0.3116 days embryo head cDNA, RIKEN full-length enrichedlibrary, clone:C130083B21 product

1700029I01Rik 2.68 RIKEN cDNA 1700029I01 gene (1700029I01Rik) Hspa4 0.31 heat shock 70 kDa protein 4Rnf13 2.66 AK037961 0.31

16 days neonate thymus cDNA, RIKEN full-lengthenriched library

Fbxl5 2.62 F-box and leucine-rich repeat protein 5 Ptpn13 0.32 protein tyrosine phosphatase, non-receptor type 13Crot 2.58 carnitine O-octanoyltransferase Mll3 0.32 mixed-lineage leukemia 3 proteinRbbp9 2.52 retinoblastoma binding protein 9 AK036133 0.33

16 days neonate cerebellum cDNA, RIKEN full-lengthenriched library, clone:9630038H04 product:

Zfp386 2.50 Zbtb38 0.33Fgd4 2.48

7 days neonate cerebellum cDNA, RIKEN full-lengthenriched library, clone:A730008H17 Ankrd15 0.33 ankyrin repeat domain 15

Gpbp1 2.46 GC-rich promoter binding protein 1 5830411J07Rik 0.33adult male thymus cDNA, RIKEN full-length enrichedlibrary, clone:5830411J07 product

Ppp3r1 2.40 protein phosphatase 3, regulatory subunit B, alpha isoform A_52_P748402 0.33 UnknownCbfb 2.39 core binding factor beta Irf6 0.33 interferon regulatory factor 6Lypla1 2.37 lysophospholipase 1 Fkbp11 0.33 FK506 binding protein 11Bzw1 2.35 basic leucine zipper and W2 domains 1 A630026N12Rik 0.33

3 days neonate thymus cDNA, RIKEN full-length enrichedlibrary, clone:A630026N12 product

Snap23 2.34 synaptosomal-associated protein 23 AK084172 0.33 heterogeneous nuclear ribonucleoprotein CPdia6 2.19 D930031A20Rik 0.34

15 days embryo head cDNA, RIKEN full-length enrichedlibrary, clone:D930031A20 product

AK044177 0.3410 days neonate cortex cDNA, RIKEN full-length enrichedlibrary, clone:A830097K04 product

Jarid1a 0.34 retinoblastoma binding protein 2AK036308 0.34

16 days neonate cerebellum cDNA, RIKEN full-lengthenriched library

Gspt1 0.35 G1 to phase transition 1NAP027922-1 0.35 UnknownA_51_P445924 0.35 UnknownAK075660 0.35

18-day embryo whole body cDNA, RIKEN full-lengthenriched library, clone:1110055F23 product

AK086528 0.3515 days embryo head cDNA, RIKEN full-length enrichedlibrary, clone:D930034N17 productENSMUST00000081

163 0.35 similar to 60S ribosomal protein L23aUevld 0.35

16 days embryo lung cDNA, RIKEN full-length enrichedlibrary, clone:8430408E05 product

Zfp398 0.35 KIAA1339 proteinAnp32b 0.35

PROLIFERATION RELATED ACIDIC LEUCINE RICHPROTEIN PAL31

AK031330 0.35 NIMA (never in mitosis gene a)-related expressed kinase 12610207I05Rik 0.35 RIKEN cDNA 2610207I05 gene2410003J06Rik 0.36

ES cells cDNA, RIKEN full-length enriched library,clone:2410003J06 product

Ppme1 0.36 protein phosphatase methylesterase 1AK046453 0.36

adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone

TC1469328 0.36 UnknownSlc43a2 0.36 solute carrier family 43, member 2Lpp 0.36 similar to TYROSINE-PROTEIN KINASE JAK3Kalrn 0.37

9 days embryo whole body cDNA, RIKEN full-lengthenriched library, clone:D030062G07 product

NAP113376-1 0.37 UnknownEtnk1 0.37

ETHANOLAMINE KINASE (EC 2.7.1.82) (EKI)homolog

AK079518 0.3716 days neonate thymus cDNA, RIKEN full-lengthenriched library, clone:A130096H23 product

Pan3 0.374 days neonate male adipose cDNA, RIKEN full-lengthenriched library, clone:B430311O07 product

A930028L21Rik 0.37adult retina cDNA, RIKEN full-length enriched library,clone:A930028L21 product

AK089714 0.37activated spleen cDNA, RIKEN full-length enrichedlibrary, clone:F830010E14 product

LOC620306 0.37adult male aorta and vein cDNA, RIKEN full-lengthenriched library, clone:A530060J09 product

Wnk1 0.38AK046930 0.38 histocompatibility 2, T region locus 180610009O20Rik 0.38 RIKEN cDNA 0610009O20 geneBC037112 0.38 cDNA sequence BC037112NP377814 0.38 mitogen activated protein kinase kinase kinase 56430706D22Rik 0.39 RIKEN cDNA 6430706D22 geneSesn3 0.39

12 days embryo eyeball cDNA, RIKEN full-lengthenriched library, clone:D230018D13 product

AK081910 0.39 weakly similar to MHC CLASS I T7 ANTIGEN2810055G22Rik 0.40 RIKEN cDNA 2810055G22 geneE030045M14Rik 0.40

0 day neonate lung cDNA, RIKEN full-length enrichedlibrary, clone:E030045M14 product

D4Ertd681e 0.4011 days embryo gonad cDNA, RIKEN full-length enrichedlibrary, clone:7030402E17 product

B230208H17Rik 0.40 RIKEN cDNA B230208H17 geneCopz1 0.40

10 days neonate skin cDNA, RIKEN full-length enrichedlibrary, clone:4732444B01 product

Snx15 0.40 sorting nexin 15AK050756 0.40

9 days embryo whole body cDNA, RIKEN full-lengthenriched library, clone:D030017D04 product

Taf3 0.40TAF3 RNA polymerase II, TATA box binding protein(TBP)-associated factor

Ubxd8 0.4112 days embryo spinal ganglion cDNA, RIKEN full-lengthenriched library, clone:D130067L24 product

Supplementary Table 2Genes exhibiting 2-fold or greater increase or decrease in ICR surrogate mother pup liver.

gene name fold change description gene name fold change descriptionIncreased in brainAK082480 27.73 RIKEN full-length enriched library,clone:C230053P15 Evx2 6.35 Homeobox even-skipped homolog protein 22310002J21Rik 23.38 RIKEN cDNA 2310002J21 gene Cpb2 6.33 Carboxypeptidase B2 precursor9530091C08Rik 20.57 RIKEN full-length enriched library,clone:4732444G10 AI840334 6.32 cDNA clone UI-M-AJ0-abd-d-05-0-UI9530083O12Rik 19.58 RIKEN full-length enriched library,clone:9530083O12 Aco2 6.24 Aconitate hydratase, mitochondrial precursorAK034271 17.29 RIKEN full-length enriched library,clone:9330171B01 Kif12 6.23 Kinesin-like protein KIF12.Nipbl 17.00 Nipped-B-like protein TC1435238 6.09 Q9ERK2 Neprilysin-like peptidase gammaPou5f2 16.83 POU domain class 5, transcription factor 2 LOC574530 6.04 metallothionein 1K (LOC574530), mRNAMyt1l 16.48 Myelin transcription factor 1-like protein Man2b1 6.01 Lysosomal alpha-mannosidase precursor (EC 3.2.1.24)

(Mannosidase, alpha B) (Lysosomal acid alpha-Pbx1 15.70 Pre-B-cell leukemia transcription factor 1 A_51_P320477 5.96 UnknownAK153595 15.54 RIKEN full-length enriched library,clone:A630010G17 Sprr4 5.93 Small proline-rich protein 4.Ccdc88a 15.39 coiled coil domain containing 88A 3110021N24Rik 5.83 RIKEN full-length enriched library,clone:2610002D035330430C04Rik 14.35 RIKEN full-length enriched library,clone:5330430C04 Ccdc33 5.81 Coiled-coil domain-containing protein 33A430106J12Rik 14.00 GRDN_MOUSE Isoform 2 of Q5SNZ0 - Mus musculus Olfr127 5.81 olfactory receptor 127AK036140 13.98 RIKEN full-length enriched library,clone:9630039A10 Olfr1360 5.80 olfactory receptor 1360Ptbp2 13.51 Polypyrimidine tract-binding protein 2 AK054225 5.78 RIKEN full-length enriched library,clone:E230034O05Camk1d 13.21 Calcium/calmodulin-dependent protein kinase ID Angptl7 5.76 Angiopoietin-related protein 7 precursorAK050741 12.15 RIKEN full-length enriched library,clone:D030014A11 Chrm4 5.70 Muscarinic acetylcholine receptor M4AK032269 11.56 RIKEN full-length enriched library,clone:6430514A06 AK089569 5.67 RIKEN full-length enriched library,clone:F830002F05Prickle2 11.48 Prickle-like protein 2. Terc 5.63 telomerase RNA component (Terc) on chromosome 3Akap9 10.42 A kinase (PRKA) anchor protein (yotiao) 9 3110009E18Rik 5.60 RIKEN cDNA 3110009E18 geneAnkrd12 10.16 ankyrin repeat domain 12 Pcdh12 5.59 Protocadherin-12 precursorBC008163 9.79 cDNA sequence BC008163 Syt6 5.59 Synaptotagmin-6Dnajb8 9.23 DnaJ homolog subfamily B member 8 (mDJ6). Pvrl4 5.58 Poliovirus receptor-related protein 4 precursorA_51_P311836 8.90 Unknown Cd74 5.54 CD74 antigenA_51_P327496 8.27 Unknown TC1482479 5.50 Unknown4930567H12Rik 7.91 RIKEN full-length enriched library,clone:4930567H12 5830472F04Rik 5.48 RIKEN full-length enriched library,clone:5830472F04Bcl2l14 7.86 Apoptosis facilitator Bcl-2-like protein 14. Trf3 5.47 TATA box binding protein like 20610039H22Rik 7.75 RIKEN full-length enriched library,clone:0610039H22 Sin3b 5.40 Paired amphipathic helix protein Sin3bAK042636 7.69 RIKEN full-length enriched library,clone:A730012J23 AK030614 5.37 RIKEN full-length enriched library,clone:5330438K19NAP056427-1 7.58 Unknown Epgn 5.34 Epigen precursorC230088H06Rik 7.51 RIKEN full-length enriched library,clone:C230088H06 Creb3l3 5.32 cAMP responsive element-binding protein 3-like protein 3Ero1lb 7.33 Endoplasmic oxidoreductin-1-like protein B TC1479199 5.25 Q7TPY4 LOC384077 protein1700018B24Rik 7.31 RIKEN full-length enriched library, clone:1700036F18 Psors1c2 5.24 Psoriasis susceptibility 1 candidate gene 2 protein homolog

precursorUpk1a 7.30 Uroplakin-1a Sh3pxd2a 5.21 SH3 and PX domain-containing protein 2APgk2 7.11 Phosphoglycerate kinase 2 BC057170 5.21 guanylate binding protein family, member 6Crisp4 7.10 cysteine-rich secretory protein 4 AK042446 5.21 RIKEN full-length enriched library,clone:A630092F23Elf4 7.03 ETS-related transcription factor Elf-4 Mitf 5.17 Microphthalmia-associated transcription factorLgr4 6.81 Leucine-rich repeat-containing G-protein coupled receptor

4 precursorA430110N23Rik 5.17 RIKEN cDNA A430110N23 gene

TC1429763 6.79 Q68J64 Glial growth factor receptor, partial L3mbtl2 5.14 Lethal(3)malignant brain tumor-like 2 protein4932415D10Rik 6.70 RIKEN cDNA B230315N10 gene TC1434594 5.13 Q9C171 Non-catalytic protein 1C730045O03Rik 6.68 RIKEN full-length enriched library, clone:C730043J07 5.12 Leucine zipper transcription factor-like 1Hrasls5 6.64 HRAS-like suppressor 5 (H-rev107-like protein 5) AK080404 5.10 RIKEN full-length enriched library,clone:A730001D016330437I11Rik 6.62 RIKEN full-length enriched library, clone:6330437I11 Setd5 5.06 SET domain-containing protein 5Hmga2 6.54 High mobility group protein HMGI-C ENSMUST0000008

48705.05 PREDICTED: similar to Ig heavy chain V-I region V35

precursor4930535E02Rik 6.52 RIKEN full-length enriched library,clone:4930535E02 Jakmip1 5.04 janus kinase and microtubule interacting protein 1Plekhn1 6.40 pleckstrin homology domain containing, family N member

1AK034785 5.01 RIKEN full-length enriched library,clone:9430037M01

Increased in liver69.83 1700034O15Rik 5.31 RIKEN cDNA 1700034O15 gene

LOC231591 22.82 PREDICTED: similar to vomeronasal 2, receptor, 1,transcript variant 1

TC1529376 5.27 UnknownC230094A16Rik 9.81 RIKEN cDNA C230094A16 gene Tex15 5.24 testis expressed gene 15Rmnd1 8.50 required for meiotic nuclear division 1 homolog Aldoa-ps1 5.23 aldolase 1, A isoform, retrogene 2Ccl19 7.25 C-C motif chemokine 19 precursor Man2b1 5.22 Lysosomal alpha-mannosidase precursorPsors1c2 6.99 Psoriasis susceptibility 1 candidate gene 2 protein homolog

precursorTbc1d19 5.22 TBC1 domain family, member 19

AK042446 6.64 RIKEN full-length enriched library,clone:A630092F23 Tert 5.17 Telomerase reverse transcriptaseOlfr1360 6.38 olfactory receptor 1360 Tmem59l 5.15 Transmembrane protein 59-like precursorBC038822 6.29 cDNA sequence BC038822 A430110N23Rik 5.12 RIKEN cDNA A430110N23 geneSlc14a2 6.03 solute carrier family 14 (urea transporter), member 2

isoform aAco2 5.12 Aconitate hydratase, mitochondrial precursor

Rtbdn 5.97 Retbindin precursor TC1519762 5.11 UnknownPcp2 5.94 Purkinje cell protein 2 Cpne1 5.11 Copine-1Ccdc33 5.91 coiled-coil domain containing 33 V1rf3 5.11 vomeronasal 1 receptor, F3Odz4 5.89 Protein Odd Oz/ten-m homolog 4 4933400E14Rik 5.10 PREDICTED: RIKEN cDNA 4933400E14 gene, transcript

variant 22310002J21Rik 5.85 RIKEN cDNA 2310002J21 gene Pcdh12 5.10 Protocadherin-12 precursorOlfr1359 5.83 olfactory receptor 1359 Rfx3 5.09 Transcription factor RFX3Rad51l3 5.77 DNA repair protein RAD51 homolog 4 Trf3 5.06 TATA box binding protein like 2Kif12 5.76 Kinesin-like protein KIF12. Gyltl1b 5.06 Glycosyltransferase-like protein LARGE2Trim68 5.60 Tripartite motif-containing protein 68 Angptl7 5.06 Angiopoietin-related protein 7 precursor1700066J24Rik 5.60 RIKEN full-length enriched library,clone:1700066J24 Arhgap12 5.06 Rho GTPase-activating protein 12TC1429763 5.59 Q68J64 (Q68J64) Glial growth factor receptor NAP068899-1 5.04 UnknownZfp383 5.49 1500001A10Rik 5.03 RIKEN cDNA 1500001A10 genePunc 5.47 Putative neuronal cell adhesion molecule precursor 3110021N24Rik 5.03 RIKEN full-length enriched library,clone:2610002D03Mast4 5.44 Microtubule-associated serine/threonine-protein kinase 4 AK054225 5.02 RIKEN full-length enriched library,clone:E230034O05Slurp1 5.40 Secreted Ly-6/uPAR-related protein 1 precursor Rnf144 5.01 Probable E3 ubiquitin-protein ligase RNF144ATet2 5.39 Mus musculus tet oncogene family member 2 Sprr4 5.01 Small proline-rich protein 4Olfr537-ps1 5.35 Olfactory receptor GA_x5J8B7TT63N-1148-873 Bmp3 5.01 Bone morphogenetic protein 3 precursorFyb 5.32 FYN-binding protein Mrps17 5.00 28S ribosomal protein S17, mitochondrial precursor

(S17mt)Gm98 5.31 RIKEN full-length enriched library,clone:D030026I12

Supplmentary Table 3Genes exhibiting 5-fold or greater decrease or increase in signals of ICSI pups neonatal tissues.

gene name fold change description gene name fold change descriptionIncreased in kidneyAK048761 11.83 RIKEN full-length enriched library,clone:C230049N15 Sin3b 5.76 Paired amphipathic helix proteinChrm4 8.73 Muscarinic acetylcholine receptor M4 A730021G18Rik 5.37 RIKEN full-length enriched library,clone:5830408F24Ptprz1 6.44 protein tyrosine phosphatase, receptor type Z, polypeptide

1Kcnj6 5.17 Potassium channel, inwardly rectifying subfamily J

member 6Sfi1 6.37 Sfi1 homolog, spindle assembly associated V1rh18 5.06 vomeronasal 1 receptor, H18A230057D06Rik 6.27 RIKEN full-length enriched library,clone:4932408B14 Hmga2 5.02 High mobility group protein HMGI-C

Decreased in brainErn1 0.06 Serine/threonine-protein kinase/endoribonuclease IRE1

precursorHoxa2 0.10 Homeobox protein Hox-A2

Fabp4 0.07 Fatty acid-binding protein, adipocyte Wfikkn1 0.12 WAP, kazal, immunoglobulin, kunitz and NTR domain-containing protein 1 precursorRyr1 0.07 ryanodine receptor 1, skeletal muscle Efr3a 0.17 Protein EFR3 homolog A (Protein EFR3-like)

TC1432492 0.08 Unknown Sall3 0.19 Sal-like protein 3Ucp1 0.09 Mitochondrial brown fat uncoupling protein 1Decreased in liverCyp1a2 0.09 Cytochrome P450 1A2 Neud4 0.10 Zinc finger protein neuro-d4Decreased in kidneyCps1 0.04 Carbamoyl-phosphate synthase Dus1l 0.10 tRNA-dihydrouridine synthase 1-likeOlfr1495 0.07 olfactory receptor 1495 Slc10a1 0.23 Sodium/bile acid cotransporterNAP052718-1 0.07 Unknown Rln1 0.29 Prorelaxin 1 precursorAK040170 0.09 RIKEN full-length enriched library,clone:A430072D23

gene name fold change description gene name fold change descriptionIncreased in brain Decreased in brainS100a5 16.89 S100 calcium binding protein A5 (S100a5) 2310038E17Rik 0.11 similar to CARBOXYLESTERASE PRECURSORClca1 14.45 chloride channel calcium activated 1 (Clca1) Npr2 0.14 natriuretic peptide receptor 2 (Npr2)Cyp2a5 14.41 cytochrome P450, family 2, subfamily a, polypeptide 5 Zfpn1a3 0.15 transcription factor aiolosTbx21 13.97 T-box 21 MGI:2384747 0.18 mRNA for erythroid differentiation regulatorCyp2a4 12.53 cytochrome P450, family 2, subfamily a, polypeptide 4 LOC545723 0.20 Hypothetical aminoacyl-transfer RNA synthetases class-IIClca2 11.71 chloride channel calcium activated 2 (Clca2) AV094648 0.20 AV094648 C57BL/6J ES cell cDNA clone 2410002B13Scgn 7.45 secretagogin, EF-hand calcium binding protein (Scgn)Hoxb6 7.28 homeo box B6 (Hoxb6)A430089I19Rik 6.93 RIKEN cDNA A430089I19 geneStoml3 6.49 stomatin (Epb7.2)-like 3 (Stoml3)LOC280121 5.44 similar to ribosomal protein P1 isoform 2, variant 1NAP101299-1 5.29Doc2g 5.19 double C2, gamma (Doc2g)Omp 5.08 Mus musculus olfactory marker protein (Omp)

Supplmentary Table 4Genes exhibiting 5-fold or greater decrease or increase in signals of ICSI mouse brain at 8 weeks.Number of genes exhibiting 2-fold or greater changes was 128.

gene name fold change description gene name fold change descriptionIncreased in brain Decreased in brainLOC667798 13.78 E030031F02Rik 0.11 13 days embryo lung cDNAHoxa7 13.75 homeo box A7 (Hoxa7) Olfr847Six3 13.57 mRNA for Six3a Ric8 0.15 15430416O09Rik 11.11 RIKEN cDNA Gabrp 0.18 rNphs2 1 nephrosis 2 homolog, podocin (human) (Nphs2) AK033926 0.20 adult male diencephalon cDNA2810038L03Rik 10, 11 days embryo whole body cDNADaf2 decay accelerating factor 2 (Daf2)AK029975 adult male testis cDNAA_52_P771912 UnknownGja8 7.71ENSMUST00000096411

0 day neonate thymus cDNAHoxc6AK037700D230015P20Rik 0 day neonate head cDNAHoxb78430419K02Rik 5.85 RIKEN cDNAA_51_P410404 UnknownTC1419200 5.51 UnknownCar3 5.10

Supplmentary Table 5Genes exhibiting 5-fold or greater decrease or increase in signals of B6 ICSI pups neonatal brain.