ENCODE Fetal development

master_table_pcg_lnc.tsv: Metadata / information about each transcript isoform (filtered for protein coding and lncRNAs only) merged.gtf: GTF of transcript isoforms transcript_tpm_summary.tsv: TPMs of each transcript isoform PFAM-Filtered-Merged.txt: PFAM domains called in each predicted ORF sequence from each transcript. Filtered for quality and confidence. dtu_results_filtered_permutations_min_samples_3.tsv: Between-organ results for differential transcript usage. Filtered for <= 0.05 FDR, for contrasts that had a permutation test signficance of <= 0.05, and for contrasts where all organs involved had > 2 samples. fetal_dhs_info.tsv - genomic locations of all DHSs, distance from nearest TSS, gene associated with nearest TSSfetal_matrix_binary.tsv - binary matrix with samples (rows) x DHSs (columns) with 1 indicating the presence of a peak in that DHS in that sample at an FDR of 1%fetal_matrix_density.tsv - matrix of read depth normalized countsfetal_matrix_vst.tsv - matrix of vst normalized counts (like deseq)fetal_meta.tsv - metadata of fetal samples, should include the ln_number for DNase, which wil match the rows of the matricies, and the per sample matching ln_number and other identifiers for short read and long read RNA seq, as indicated by the column titles dtu_pairwise_organ_max_per_gene_abs_difference_relative_abundance.tsv: For each gene and organ pair, this table reports the transcript with the largest absolute difference in mean relative abundance (its percentage of total gene expression) as well as this difference itself. dtu_pairwise_organ_abs_difference_relative_abundance.tsv: For each gene and organ pair, this table reports each transcript and it's absolute difference in mean relative abundance (its percentage of total gene expression).