Additional file 11 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 11. Code_S2

Additional file 7 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 7: Table_S5.Expression_profiling_cluster_genes

Additional file 2 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 2: Figure S2. Expression of TH pathway genes in different muscle groups. The expression of the indicated genes was estimated from the muscleDB dataset and is represented as RPKM. Data analysis was performed as for Fig. 3

Additional file 4 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 4: Table_S2.Six1_1MT_peaks(mm9).bed

Additional file 3 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 3: Table_S1.Six1_1MB_peaks(mm9).bed

Additional file 10 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 10. Code_S1

Additional file 13 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 13. Code_S4

Additional file 8 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 8: Table_S6.Primers

Additional file 5 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 5: Table_S3.Six1_1MB_peaks(mm9).annotated

Additional file 1 of Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter

Additional file 1: Figure S1. Six1 ChIP-seq results analysis. A) Example of Six1 target loci, showing the Six1 ChIP-seq read coverage in MB and MT. At the Myod1 locus, the core enhancer region (CER) is highlighted in blue and the distal regulatory region (DRR) is highlighted in green. Coverage is shown normalized to counts per million in each library and represented as the difference between the ChIP and input samples, calculated in bins of 10 base pairs. The coverage track for the negative control rabbit IgG ChIP-seq sample is also shown. For each genomic locus, all three tracks are shown at the same scale. B) ChIP-seq coverage at Six1 binding sites, separated in three groups: bound by Six1 in MB only (green), in MB and MT (beige) or MT only (orange). Coverage is shown in a 5 kb window centered on the center of the Six1 binding site. For the same groups of regions, coverage is also given for additional genomics datasets from the indicated studies: Umansky et al. ChIP-seq for c-Jun, MyoD and Runx1 in primary myoblasts (73), Asp et al. and Blum et al. histone mark ChIP-seq in C2C12 MB and MT (69,81), and Barish et al. histone marks and ATAC-seq signal in skeletal muscle groups (gastrocnemius and soleus) (80). For each antibody used (each TF or mark), the heatmap color and average plot scales are maintained so they can be directly compared