Normalization summary

The normalized ATAC-seq dataset contains accessibility profiles for 142 samples.

Signal has been normalized for the following region sets:

The plot below shows the quantile-quantile relationship of unnormalized to normalized insertion counts, overall and for each sample.

Region type

t200 t10k promoters_gc_protein_coding ERB_BP_distal ERB_BP_dnase ERB_BP_proximal ERB_BP_tfbs ERB_BP_tss .peaks.cons

Sample

[ALL] Bbulk_S_1001 Bbulk_S_1002 Bbulk_S_1003 Bbulk_U_1001 Bbulk_U_1002 Bbulk_U_1003 Bbulk_U_1004 Bmem_S_1001 Bmem_S_1002 Bmem_S_1003 Bmem_S_1010 Bmem_U_1001 Bmem_U_1002 Bmem_U_1003 Bmem_U_1004 Bnaive_S_1001 Bnaive_S_1002 Bnaive_S_1003 Bnaive_U_1001 Bnaive_U_1002 Bnaive_U_1003 Bnaive_U_1004 TCD4EM_S_1001 TCD4EM_S_1002 TCD4EM_S_1003 TCD4EM_S_1004 TCD4EM_U_1001 TCD4EM_U_1002 TCD4EM_U_1003 TCD4EM_U_1004 TCD8_S_1001 TCD8_S_1002 TCD8_S_1003 TCD8_S_1004 TCD8_U_1001 TCD8_U_1002 TCD8_U_1003 TCD8_U_1004 TCD8CM_S_1001 TCD8CM_S_1002 TCD8CM_S_1003 TCD8CM_S_1004 TCD8CM_U_1001 TCD8CM_U_1002 TCD8CM_U_1003 TCD8CM_U_1004 TCD8EM_S_1001 TCD8EM_S_1002 TCD8EM_S_1003 TCD8EM_S_1004 TCD8EM_U_1001 TCD8EM_U_1002 TCD8EM_U_1003 TCD8EM_U_1004 TCD8naive_S_1001 TCD8naive_S_1002 TCD8naive_S_1003 TCD8naive_S_1004 TCD8naive_U_1001 TCD8naive_U_1002 TCD8naive_U_1003 TCD8naive_U_1004 TeffMem_S_1001 TeffMem_S_1002 TeffMem_S_1003 TeffMem_S_1004 TeffMem_U_1001 TeffMem_U_1002 TeffMem_U_1003 TeffMem_U_1004 TeffNaive_S_1001 TeffNaive_S_1002 TeffNaive_S_1003 TeffNaive_S_1004 TeffNaive_S_1011 TeffNaive_U_1001 TeffNaive_U_1002 TeffNaive_U_1003 TeffNaive_U_1004 Tfh_S_1001 Tfh_S_1002 Tfh_S_1003 Tfh_S_1004 Tfh_U_1001 Tfh_U_1002 Tfh_U_1003 Tfh_U_1004 Tfh_U_1010 Tgd_S_1001 Tgd_S_1002 Tgd_S_1003 Tgd_S_1004 Tgd_U_1001 Tgd_U_1002 Tgd_U_1003 Tgd_U_1004 Th17prec_S_1001 Th17prec_S_1002 Th17prec_S_1003 Th17prec_S_1004 Th17prec_U_1001 Th17prec_U_1002 Th17prec_U_1003 Th17prec_U_1004 Th1prec_S_1001 Th1prec_S_1002 Th1prec_S_1003 Th1prec_S_1004 Th1prec_U_1001 Th1prec_U_1002 Th1prec_U_1003 Th1prec_U_1004 Th2prec_S_1001 Th2prec_S_1002 Th2prec_S_1003 Th2prec_S_1004 Th2prec_U_1001 Th2prec_U_1002 Th2prec_U_1003 Th2prec_U_1004 Treg_S_1001 Treg_S_1002 Treg_S_1003 Treg_S_1004 Treg_U_1001 Treg_U_1002 Treg_U_1003 Treg_U_1004 TregMem_S_1001 TregMem_S_1002 TregMem_S_1003 TregMem_S_1004 TregMem_U_1001 TregMem_U_1002 TregMem_U_1003 TregMem_U_1004 TregNaive_S_1004 TregNaive_S_1010 TregNaive_U_1001 TregNaive_U_1002 TregNaive_U_1004 TregNaive_U_1008

Figure 1

QQ-plot of unnormalized vs normalized counts

The heatmaps below show the unnormalized and normalized insertion counts at each quantile for each sample in the dataset.

Region type

t200 t10k promoters_gc_protein_coding ERB_BP_distal ERB_BP_dnase ERB_BP_proximal ERB_BP_tfbs ERB_BP_tss .peaks.cons

Figure 2

Heatmaps of unnormalized vs normalized counts for each quantile and sample