Extended Data Fig. 9: STARR-seq and reporter assay in oocytes.

a, Schematic of STARR-seq in FGOs. 70 candidates and 16 negative controls were manually cloned into the STARR-seq constructs and then the pooled products were injected into the nuclei of FGOs. The RNA was recovered by a method adapted from Smart-seq2 (ref. ⁵⁴) (Methods) to suit low-input cells, followed by sequencing. b, Scatter plots showing STARR-seq signals (RNA output vs. DNA input) (Methods) in both replicates and strands. Red, enhancer candidates; blue, negative control elements. c, UCSC genome browser showing FGO STARR-seq RNA output and DNA input signals on chromosome 16. d, Heatmaps showing STARR-seq (STARR/input) signals in FGO with two replicates and Pol II signals in GO-P14 and FGO at enhancer candidates and negative control regions. e. Top, fluorescence and bright fields of mouse FGOs in an enhancer reporter assay (Pro, mini promoter). Scale bar, 100 μm. Bottom, boxplot showing the ratio of GFP to mCherry intensity in the enhancer reporter assay. The dashed line indicates the ratio in the empty vector group. The numbers of oocytes used in each group: 17, 14, 17, 18, 10, 18, 15, 17, 13, 10, 12, 19, 11, and 6. The median is indicated by the center line. The bottom, top edges, and whiskers represent the 10th and 90th percentiles and 1.5 times the interquartile range (IQR), respectively. Source numerical data and unprocessed blots are available in source data.