Supplementary Information for

Tables

• Supplementary Table 1    Expression, and differential expression, of 527 ovarian germ-cell-enriched genes,as well as all Refseq annotated genes, in E12.5, E14.5, and E16.5 in wild-type (Kit+/Kit+)and germ-cell-depleted (KitW/KitWv) ovary and testis.
• Supplementary Table 2    Expression, and differential expression, of 104 meiotic prophase-specific genes,as well as all Refseq annotated genes, in E14.5 wild-type,Stra8-deficient, andDazl-deficient ovary.
• Supplementary Table 3    Correlation coefficients for expression of meiotic prophase genes against Rec8.
• Supplementary Table 4    Expression, and differential expression, of 527 ovarian germ-cell-enriched genesin anterior and posterior thirds of E12.5 and E13.5 wild-type ovary.

Files

• Supplementary Text Published data on fertility and/or meiotic defects for 104 meiotic prophase-spe-cific genes.

Figures

• Figure S1: Rec8is expressed in both somatic and germ cells. E14.5 fetal ovaries stained withDAPI, and for SSEA1 (immunofluorescence),Rec8(single molecule fluorescent in situ hybrid-ization, smFISH), andDazl(smFISH). Single transcripts ofRec8andDazlare detected as punctate signals by smFISH. Germ cells are outlined in red.
• Figure S2: Transcript densities of meiotic prophase genes as measured by single moleculeFISH. (A) Violin plots representing distribution of transcript densities in wild type (red),Stra8mutant (blue) andDazlmutant (green), for 13 selected meiotic prophase genes. Asterisks rep-resent significant differences between the means of distributions (t-test on average transcriptdensity of a population of germ cells from independent biological replicates). n.s. denotes dif-ferences that are not statistically significant (p>0.05). ForMei1andMsh5, expression inStra8andDazlmutants averaged less than 1 transcript per cell, so differences betweenStra8andDazlmutants were not tested. Genes were grouped into class 1, 2, and 3 based on significantdifferences in expression between wild-type,Stra8-deficient, andDazl-deficient germ cells asdescribed in main text.Sycp2transcript densities do not differ significantly between wild-type andStra8-deficient germ cells. Nevertheless, we placed it in class 2 based on subsequent analy-ses that show that by E15.5, it is expressed at significantly lower levels inStra8-deficient com-pared to wild-type germ cells (S3 Fig, p = 0.0088 at E15.5). (B) Scatterplot of log2 fold-changeof gene expression in E14.5Stra8mutant over wild-type ovary againstDazlmutant over wild-type ovary for 104 meiotic prophase genes, as measured by RNA-seq. Thirteen selected meioticprophase genes that were also examined by smFISH are highlighted in color. Red, orange, andyellow represent class 1, 2, and 3 genes respectively, as defined by smFISH.
• Figure S3: Single cell correlation of expression of meiotic prophase genes compared toRec8inStra8-deficient ovaries.Representative scatterplots of transcript densities of 12 meiotic pro-phase genes from class 2 and 3 (y-axis) againstRec8(x-axis) as measured in E14.5Stra8-defi-cient ovaries. Correlation coefficients for both plots shown, and for biological replicates, aregiven inS3 Table.
• Figure S4: Correlation of change over time versus anterior-posterior position.Scatterplot oflog2 fold-change in expression of 527 ovarian germ-cell-enriched genes in time (E13.5 anteriorover E12.5 anterior) versus space (E13.5 anterior over E13.5 posterior). Source data is provided inS4 Table.
• Figure S5: Spatiotemporal analyses of gene expression by single molecule FISH.Spatiotemporalplot of average transcript densities of class 2 and 3 genes along anterior-posterior axis of theovary at E11.5, E12.5, E13.5, E14.0, E14.5, E15.0, E15.5, and E16.5. (Rec8andSycp3are shown inFig 4.)
• Figure S6: Single molecule FISH analyses ofStra8andStra8-lacZreporter.Representative scat-terplot of transcript densities ofStra8-lacZreporter (y-axis) againstStra8(x-axis) from E14.5Stra8wild type/lacZheterozygote, showing correlation oflacZandStra8expression.