Additional data supporting "Efficient profiling of total RNA in single cells with STORM-seq"

Additional source data supporting "Efficient profiling of total RNA in single cells with STORM-seq" Within this repo are additional intermediate data objects and genomic references that can be used for the results shown in the paper. Within the zip directory are the following files: ```zenodo_data_upload/├── ens101_ercc92_repeatmasker_refs - genomic references used in the text│ ├── Homo_sapiens.GRCh38.101.ercc92patched.gtf.gz│ ├── Homo_sapiens.GRCh38.dna.primary_assembly_ercc92.fa.fai.gz│ ├── Homo_sapiens.GRCh38.dna.primary_assembly_ercc92.fa.gz│ └── repeatmasker_repeatlib_20140131_hg38.fa.out.gz├── ercc_detection - additional data objects used for each subsampled depth for ERCC detection│ ├── storm_100k_sce_filt_hg38_ens101.rds│ ├── storm_1M_filt_sce_ens101_kb.rds│ ├── storm_250k_filt_sce_ens101.rds│ └── storm_500k_filt_sce_gene_kb_ens101.rds├── erna - many additional intermediate objects and files supporting the eRNA expression profiling│ ├── D14_soloAligned.sortedByCoord.out.bam│ ├── GSM4610686_L_K562_Rep1.coverage.track.combined_fwd_rev.no_chr.bw│ ├── GSM4610686_L_K562_Rep1.coverage.track.minus_no_chr.pints_distal_grocap_intergenic.data_matrix.tab│ ├── GSM4610686_L_K562_Rep1.coverage.track.plus_no_chr.pints_distal_grocap_intergenic.data_matrix.tab│ ├── GSM4610687_L_K562_Rep2.coverage.track.combined_fwd_rev.no_chr.bw│ ├── GSM4610687_L_K562_Rep2.coverage.track.minus_no_chr.pints_distal_grocap_intergenic.data_matrix.tab│ ├── GSM4610687_L_K562_Rep2.coverage.track.plus_no_chr.pints_distal_grocap_intergenic.data_matrix.tab│ ├── I17_soloAligned.sortedByCoord.out.bam│ ├── J5_soloAligned.sortedByCoord.out.bam│ ├── merged_storm_k562_solo_pints_aligned.sorted.bpm_norm.fwd.data_matrix.tab│ ├── merged_storm_k562_solo_pints_aligned.sorted.bpm_norm.rev.data_matrix.tab│ ├── merged_vasa_starsolo_pints_groprocap_distal_enh.ens101.fwd.pints_groprocap_distal_enh.bpm_norm.data_matrix.tab│ ├── merged_vasa_starsolo_pints_groprocap_distal_enh.ens101.rev.pints_groprocap_distal_enh.bpm_norm.data_matrix.tab│ ├── pints_k562_resources - downloaded and parsed from https://pints.yulab.org/│ │ └── Distal_K562_gro_pro_cap_pints_hg38_gencode24.only_regions.bed│ ├── pro_cap_encode_reps1_2_ave_minus_strand.pints_distal_1kbfilt_expand.data_matrix.tab│ ├── pro_cap_encode_reps1_2_ave_plus_strand.pints_distal_1kbfilt_expand.data_matrix.tab│ ├── storm_150k_filt_sce_with_pints_distal_groprocap_k562_enh_annots_hg38_ens101.rds│ └── vasa_plate_150k_filt_sce_with_pints_distal_groprocap_k562_enh_annots_hg38_ens101.rds├── fallopian_tube - the main set of objects used throughout the fallopian tube analyses│ ├── ss2│ │ └── ss2_salmon_ens102_requant_grch38_velocessor_normd_data_with_geneids_with_embeddings.rds│ └── storm│ ├── cryo_fte_hiseq_grch38_salmon_norm_se_with_embeddings_forscvelo.h5ad - for scvelo│ ├── cryo_fte_hiseq_grch38_salmon_norm_se_with_embeddings_forscvelo.rds│ ├── cryo_fte_hiseq_grch38_salmon_norm_se_with_embeddings.rds - main object donor 2│ ├── cryo_fte_novasseq_grch38_salmon_norm_se_with_embeddings_forscvelo.h5ad - for scvelo│ ├── cryo_fte_novasseq_grch38_salmon_norm_se_with_embeddings_forscvelo.rds│ ├── cryo_fte_novasseq_grch38_salmon_norm_se_with_embeddings.rds - main object donor 1│ ├── donor_1_novaseq_index_sort.txt - cell surface marker fluorescence│ ├── donor_2_hiseq_index_sort.txt - cell surface marker fluorescence│ ├── mnn_ss2_storm_image_20210412.rda│ ├── mnn_storm_integration_20210412.rda - MNN integrated donors 1 and 2 STORM-seq│ └── principle_curves_pat1_pat2_with_pseudotime_20250616.rda - principal curves├── feature_comparison│ ├── cell_cell_cors│ │ └── storm_1M_gene_txps_raw_kb.rda│ ├── gene_body_cov│ │ ├── hek293t_merged_five_prime_r1_only.geneBodyCoverage.txt│ │ ├── hek293t_merged_internal_reads.geneBodyCoverage.txt│ │ ├── ss2_750k_hek293t_merged.geneBodyCoverage.txt│ │ ├── sstotal_750k_genebody_proteincoding_ens101.geneBodyCoverage.txt│ │ ├── storm_750k_genebody_proteincoding_ens101.geneBodyCoverage.txt│ │ ├── tenx_hek293t_genebody_proteincoding_ens101.geneBodyCoverage.txt│ │ └── vasa_750k_genebody_proteincoding_ens101.geneBodyCoverage.txt│ ├── gene_counts│ │ ├── ss3x│ │ │ ├── ss3xpress_gene_txp_counts_ens101_with_erccs_for_plotting.rds│ │ │ └── ss3xpress_raw_complexity_curve_gene_txp_counts_ens101_with_erccs.rds│ │ ├── sstotal│ │ │ ├── sstotal_gene_txp_counts_ens101_with_erccs_for_plotting.rds│ │ │ └── sstotal_raw_complexity_curve_gene_txp_counts_ens101_with_erccs.rds│ │ ├── storm│ │ │ ├── storm_gene_txp_counts_ens101_with_erccs_for_plotting.rds│ │ │ ├── storm_hek_complexity_curve_to_plot.rds│ │ │ ├── storm_raw_complexity_curve_gene_txp_counts_ens101_with_erccs.rds│ │ │ └── well_map.txt│ │ └── vasa│ │ ├── vasa_gene_txp_counts_ens101_with_erccs_for_plotting.rds│ │ └── vasa_raw_complexity_curve_gene_txp_counts_ens101_with_erccs.rds│ ├── mapping_rates│ │ └── mapping_rates_20240125_kb.rda│ └── txp_isoforms│ ├── bulk_rep1_abundance.tsv.gz│ ├── bulk_rep2_abundance.tsv.gz│ ├── storm_rep1_abundance.tsv.gz│ ├── storm_rep2_abundance.tsv.gz│ └── vasa_abundance.tsv.gz├── gene_fusions│ ├── bulk_k562_full_depth_star_fusion_agg_deconv.fusions.abridged.tsv.gz│ ├── K562_fusions.csv.gz│ ├── k562_mrna_star-fusion.fusion_predictions.abridged.tsv.gz│ ├── ss3xpress_internal_150k_depth_star_fusion_agg_deconv.fusions.abridged.tsv.gz│ ├── star_fusion_vasa_plateSE_150k_agg_deconv.fusions.abridged.tsv.gz│ └── storm_star_fusion_150k_depth_k562_agg_deconv.fusions.abridged.tsv.gz├── genomic_region_analysis│ ├── Homo_sapiens.GRCh38.dna.primary_assembly_ercc92_dnastringset.rds│ ├── merged_bulk_100k_ds_tworep_nonannot.sorted.converted_frags.bed.gz│ ├── merged_bulk_100k_mapqfilt_nonannot_reads.bam│ ├── merged_hek293t_nonannot_reads.sorted.bed.gz│ ├── merged_hek293t_sstotal_mismapped.sorted.bed.gz│ ├── merged_hek293t_storm_nonannot_reads_ens101.sorted.converted_frags.bed.gz│ ├── merged_nonannot_reads_ss3xpress_ens101.sorted.converted_frags.bed.gz│ ├── merged_ss3_nonannot_reads_mapqfilt_100k.bam│ ├── merged_sstotal_umi_nonannot_reads_100k_mapqfilt.sorted.bam│ ├── merged_storm_100k_nonannot_reads.bam│ ├── merged_vasa_nonannot_100k_mapqfilt_reads.bam│ ├── rloop_hg38_all_rlhub.bed.gz│ └── rloop_hg38_forming_seqs_rlhub.bed.gz├── polyA_and_polyT_tracks│ ├── hg38_polyA_min6_c2_at_filt.bed.gz│ ├── hg38_polyA_min6_c2_at_filt.bed.gz.tbi│ ├── hg38_polyT_min6_c2_at_filt.bed.gz│ └── hg38_polyT_min6_c2_at_filt.bed.gz.tbi├── seq_logos│ ├── umi_frequencies_all_technologies.tsv.gz│ ├── umi_most_abundant_all_technologies.tsv│ └── unique_umi_diversity_all_technologies.tsv├── te_quantification│ ├── bulk_storm_vasa_sstotal_hek_merged_te_quants_cpm.txt.gz│ ├── donor1_novaseq_fte_te_cpm_sce_ens101_ten_perc_filt_line_sine_ltr.rds│ ├── donor2_hiseq_fte_te_cpm_sce_ens101_pat1_te_markers_with_embeddings.rds│ ├── fte_te_heatmap_marker_tes.txt│ ├── intergenic_intronic_tes.txt.gz│ ├── total_rna_te_expression_cpm_analysis_hek_line_sine_ltr.rds│ ├── wgcna_tes_genes_donor1_blockwise.rda│ └── wgcna_tes_projected_mes_donor2.rda├── te_txp_stitching│ ├── 2023_nat_gen_shah_et_al_oncoexap_k562│ │ └── curated_known_events.txt.gz│ ├── bulk│ │ ├── teprof3_output_filter_transcript_TE_transcript_consensus.tsv.gz│ │ └── teprof3_output_quantification.TE.tsv.gz│ ├── storm│ │ ├── mono_exons_with_header.txt.gz│ │ ├── purpl_split_bams│ │ │ ├── purpl_gene_annots_with_tes_ens101.gtf│ │ │ ├── storm_pseudobulk_purpl_splitreads.bam│ │ │ ├── storm_pseudobulk_purpl_splitreads.bam.bai│ │ │ ├── storm_pseudobulk_purpl.bam│ │ │ └── storm_pseudobulk_purpl.bam.bai│ │ ├── qcd_k562_cells_for_downstream_analyses.txt.gz│ │ ├── storm_rds_and_remap│ │ │ ├── storm_raw_complexity_curve_gene_txp_counts_ens101_with_erccs.rds│ │ │ └── well_map.txt│ │ ├── teprof3_output_filter_transcript_TE_transcript_consensus.tsv.gz│ │ ├── teprof3_output_quantification.TE.storm_qc_cell_filt.tsv.gz│ │ └── teprof3_output_quantification.TE.tsv.gz│ └── TEProf3_resources│ ├── gene_annotation.gtf.gz│ ├── gene_exon_annotation_sorted.txt.gz│ ├── gene_exon_coordinates_annotation.txt.gz│ ├── gene_exon_intron_annotation_sorted.txt.gz│ ├── gene_intron_coordinates_annotation.json│ ├── gene_start_codon_annotation_sorted.txt.gz│ ├── gene_transcript_annotation_sorted.txt.gz│ ├── herv_annotation.txt.gz│ ├── HERV.gtf.gz│ ├── LINE1.bed.gz│ ├── repeatmasker_sorted.bed.gz│ ├── repeatmasker_sorted.pints_filt.bed.gz│ └── repeatmasker_sorted.txt.gz└── txp_variance_analysis └── txp_var_robustness_image_storm_seq.rda```