Looper PEPPRO summary

Stats summary file
sample_name sample_desc treatment replicate toggle protocol organism read_type cell_type purpose umi_status umi_length data_source read1 srr srx Sample_title Sample_geo_accession Sample_source_name_ch1 Sample_characteristics_ch1 Sample_extract_protocol_ch1 Sample_description Sample_data_processing Sample_platform_id Sample_contact_name Sample_contact_email Sample_contact_laboratory Sample_contact_department Sample_contact_institute Sample_contact_address Sample_contact_city Sample_contact_zip/postal_code Sample_contact_country Sample_instrument_model Sample_library_selection Sample_library_source Sample_library_strategy Sample_relation gsm_id Sample_supplementary_file_1 Sample_supplementary_file_2 Sample_series_id File_mb Read_type Genome Raw_reads Fastq_reads Reads_with_adapter Uninformative_adapter_reads Pct_uninformative_adapter_reads Trimmed_reads Trim_loss_rate Peak_adapter_insertion_size Degradation_ratio Aligned_reads_human_rDNA Alignment_rate_human_rDNA Mapped_reads QC_filtered_reads Aligned_reads Alignment_rate Total_efficiency Read_depth Mitochondrial_reads Maximum_read_length Genome_size NRF PBC1 PBC2 Unmapped_reads TSS_coding_score TSS_non-coding_score Pause_index Plus_FRiP Minus_FRiP mRNA_contamination Time Success Duplicate_reads Frac_exp_unique_at_10M read2
K562_PRO-seq K562 PRO-seq none 1 1 PRO human SINGLE K562 gold standard FALSE 0 SRA /project/shefflab/data/sra_fastq/SRR1554311.fastq.gz /pro... SRR155431[1-2] SRX683602 K562 PRO-Seq GSM1480327 K562 cells pull-down substrate: streptavidin PRO-seq libraries were prepared as described previously (... This Sample represents two sequencing replicates. Supplementary_files_format_and_content: Processed data fi... GPL16791 Leighton,James,Core ljc37@cornell.edu John T. Lis Moleular Biology and Genetics Cornell University 417 Biotechnology Building Ithaca 14853 USA Illumina HiSeq 2500 other transcriptomic OTHER SRA: https://www.ncbi.nlm.nih.gov/sra?term GSM1480327 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1480nnn/GSM1480... ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1480nnn/GSM1480... GSE60456 38517.59 single hg38 496581677 496581677 423059183.0 12437983.0 2.5047 484143694 2.5 34 0.2312 44680364.0 9.23 434069790 46741044 387328746 80.0 78.0 29.61 9149071 100 3099922541 0.28 0.54 3.89 5393540 13.9 5.8 10.8 0.36 0.34 1.37 13:05:37 02-27-22:28:40 NA NA NA
K562_RNA-seq_10 90% K562 PRO-seq + 10% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_10pct_RNArc_r2.fastq.gz K562_10pct_RNArc_r2 NA K562 RNA spike-in 10pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 806.57 single hg38 10000000 10000000 8011909.0 224478.0 2.2448 9775522 2.24 34 0.2306 833666.0 8.53 8700764 1036653 7664111 78.4 76.64 1.98 227220 100 3099922541 0.95 0.98 50.04 241092 15.6 5.6 13.88 0.36 0.34 2.06 1:02:06 02-27-10:25:08 NA NA NA
K562_RNA-seq_20 80% K562 PRO-seq + 20% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_20pct_RNArc_r2.fastq.gz K562_20pct_RNArc_r2 NA K562 RNA spike-in 20pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 806.51 single hg38 10000000 10000000 7511497.0 199835.0 1.9984 9800165 2.0 34 0.2305 768600.0 7.84 8644667 1123750 7520917 76.74 75.21 2.05 267632 100 3099922541 0.94 0.97 49.21 386898 15.9 5.3 13.46 0.36 0.35 2.63 1:01:28 02-27-10:24:31 NA NA NA
K562_RNA-seq_30 70% K562 PRO-seq + 30% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_30pct_RNArc_r2.fastq.gz K562_30pct_RNArc_r2 NA K562 RNA spike-in 30pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 803.62 single hg38 10000000 10000000 7013383.0 174726.0 1.7473 9825274 1.75 34 0.2303 703191.0 7.16 8597206 1214446 7382760 75.14 73.83 2.15 309258 100 3099922541 0.93 0.97 46.16 524877 16.2 5.3 13.1 0.37 0.36 3.21 0:57:50 02-27-10:21:26 NA NA NA
K562_RNA-seq_40 60% K562 PRO-seq + 40% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_40pct_RNArc_r2.fastq.gz K562_40pct_RNArc_r2 NA K562 RNA spike-in 40pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 800.5 single hg38 10000000 10000000 6515223.0 149598.0 1.496 9850402 1.5 34 0.2301 638008.0 6.48 8549090 1305366 7243724 73.54 72.44 2.26 351192 100 3099922541 0.91 0.97 41.7 663304 16.7 5.0 12.91 0.37 0.36 3.83 1:13:24 02-27-10:36:56 NA NA NA
K562_RNA-seq_50 50% K562 PRO-seq + 50% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_50pct_RNArc_r2.fastq.gz K562_50pct_RNArc_r2 NA K562 RNA spike-in 50pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 796.96 single hg38 10000000 10000000 6017590.0 124631.0 1.2463 9875369 1.25 34 0.2304 573409.0 5.81 8499876 1395808 7104068 71.94 71.04 2.41 393154 100 3099922541 0.89 0.96 36.68 802084 17.0 4.7 12.83 0.38 0.37 4.6 1:05:47 02-27-10:29:22 NA NA NA
K562_RNA-seq_60 40% K562 PRO-seq + 60% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_60pct_RNArc_r2.fastq.gz K562_60pct_RNArc_r2 NA K562 RNA spike-in 60pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 793.14 single hg38 10000000 10000000 5519636.0 99594.0 0.9959 9900406 1.0 34 0.2307 508442.0 5.14 8452082 1486236 6965846 70.36 69.66 2.6 434938 100 3099922541 0.86 0.95 31.45 939882 17.1 4.3 12.56 0.38 0.38 5.45 1:04:08 02-27-10:28:10 NA NA NA
K562_RNA-seq_70 30% K562 PRO-seq + 70% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_70pct_RNArc_r2.fastq.gz K562_70pct_RNArc_r2 NA K562 RNA spike-in 70pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 788.96 single hg38 10000000 10000000 5020699.0 74592.0 0.7459 9925408 0.75 34 0.2307 443714.0 4.47 8403304 1577377 6825927 68.77 68.26 2.86 477155 100 3099922541 0.83 0.94 26.62 1078390 17.6 3.9 12.41 0.39 0.38 6.57 1:03:23 02-27-10:27:24 NA NA NA
K562_RNA-seq_80 20% K562 PRO-seq + 80% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_80pct_RNArc_r2.fastq.gz K562_80pct_RNArc_r2 NA K562 RNA spike-in 80pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 784.39 single hg38 10000000 10000000 4521696.0 49637.0 0.4964 9950363 0.5 34 0.2303 378416.0 3.8 8355005 1668539 6686466 67.2 66.86 3.21 519002 100 3099922541 0.8 0.93 22.13 1216942 18.1 3.6 12.25 0.39 0.39 8.02 1:03:13 02-27-10:27:16 NA NA NA
K562_RNA-seq_90 10% K562 PRO-seq + 90% K562 RNA-seq none 1 1 PRO human SINGLE K562 mRNA contamination; FRiF/PRiF FALSE 0 SRA /project/shefflab/data/guertin/fastq/K562_90pct_RNArc_r2.fastq.gz K562_90pct_RNArc_r2 NA K562 RNA spike-in 90pct RC GSM1480327;GSM765405 K562 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 779.46 single hg38 10000000 10000000 4024168.0 24881.0 0.2488 9975119 0.25 34 0.23 313360.0 3.14 8305810 1759025 6546785 65.63 65.47 3.75 560951 100 3099922541 0.76 0.91 18.23 1355949 18.6 3.2 12.14 0.4 0.4 10.06 1:02:06 02-27-10:26:37 NA NA NA
K562_GRO-seq K562 GRO-seq none 1 1 GRO human SINGLE K562 degraded library; low pause index FALSE 0 SRA /project/shefflab/data/sra_fastq/SRR1552484.fastq.gz SRR1552484 SRX682020 K562 GRO-seq GSM1480325 K562 cells antibody: anti-BrU (Santa Cruz Biotechnology, sc-32323-ac... GRO-seq libraries were prepared as in Core et al. (Core, ... cDNA (from nascent RNA) Supplementary_files_format_and_content: Processed data fi... GPL11154 Leighton,James,Core ljc37@cornell.edu John T. Lis Moleular Biology and Genetics Cornell University 417 Biotechnology Building Ithaca 14853 USA Illumina HiSeq 2000 other transcriptomic OTHER SRA: https://www.ncbi.nlm.nih.gov/sra?term GSM1480325 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1480nnn/GSM1480... ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1480nnn/GSM1480... GSE60456 1322.25 single hg38 30363736 30363736 22296806.0 1041369.0 3.4296 29322367 3.43 22 0.7189 4309471.0 14.7 22899670 4468262 18431408 62.86 60.7 2.65 843399 50 3099922541 0.7 0.86 8.69 2113226 23.9 8.6 14.58 0.34 0.32 1.33 1:03:44 02-27-10:28:17 NA NA NA
HelaS3_GRO-seq HelaS3 GRO-seq none 1 1 GRO human SINGLE HelaS3 low pause index; high mRNA contamination; no adapter dist... FALSE 0 SRA /project/shefflab/data/sra_fastq/SRR1693611.fastq.gz /pro... SRR169361[1-2] SRX796411 HelaS3_GRO-seq GSM1558746 HelaS3_cells cell type: HelaS3 For 5’GRO-seq, immunoprecipitated RNA was dephosphorylate... run-on RNA Supplementary_files_format_and_content: bedGraph files ar... GPL16791 Scott,Allen,Lacadie scott.lacadie@mdc-berlin.de Ohler Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Robert-Rössle-Str. 10 Berlin-Buch 13092 Germany Illumina HiSeq 2500 cDNA transcriptomic RNA-Seq SRA: https://www.ncbi.nlm.nih.gov/sra?term GSM1558746 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1558nnn/GSM1558... ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1558nnn/GSM1558... GSE63872 3550.33 single hg38 72718941 72718941 22179715.0 0.0 0.0 72718941 0.0 0 0.0 40879756.0 56.22 21029691 6163527 14866164 20.44 20.44 2.34 1906316 51 3099922541 0.72 0.91 13.55 10809494 7.3 4.1 6.18 0.37 0.33 3.22 1:23:01 02-27-10:47:33 NA NA NA
Jurkat_ChRO-seq_1 Jurkat ChRO-seq none 1 1 PRO human SINGLE Jurkat degraded library true_6 6 SRA /project/shefflab/data/sra_fastq/SRR7616133.fastq.gz SRR7616133 SRX4480700 Jurkat chromatin run-on 1 [ChRO-seq] GSM3309956 Jurkat T-cells batch: 1 We prepared PRO-seq libraries as described in Kwak et. al... Jurkat chromatin run-on Supplementary_files_format_and_content: *bw: Mapped reads... GPL18573 Charles,G,Danko dankoc@gmail.com Danko Lab Baker Institute Cornell University Hungerford Hill Rd Ithaca 14853 USA Illumina NextSeq 500 other transcriptomic OTHER SRA: https://www.ncbi.nlm.nih.gov/sra?term GSM3309956 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3309nnn/GSM3309... ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3309nnn/GSM3309... GSE117832 1330.25 single hg38 37740511 37740511 34473620.0 2012355.0 5.3321 32783879 13.13 20 0.9566 3493243.0 10.66 28177350 6839271 21338079 65.09 56.54 3.87 4738 70 3099922541 0.38 0.64 3.39 1113286 55.1 12.6 50.36 0.36 0.34 1.19 1:26:16 02-27-10:51:19 14846147.0 0.7897 NA
Jurkat_ChRO-seq_2 Jurkat ChRO-seq none 2 1 PRO human SINGLE Jurkat intact library true_6 6 SRA /project/shefflab/data/sra_fastq/SRR7616134.fastq.gz SRR7616134 SRX4480701 Jurkat chromatin run-on 2 [ChRO-seq] GSM3309957 Jurkat T-cells batch: 2 We prepared PRO-seq libraries as described in Kwak et. al... Jurkat chromatin run-on Supplementary_files_format_and_content: *bw: Mapped reads... GPL18573 Charles,G,Danko dankoc@gmail.com Danko Lab Baker Institute Cornell University Hungerford Hill Rd Ithaca 14853 USA Illumina NextSeq 500 other transcriptomic OTHER SRA: https://www.ncbi.nlm.nih.gov/sra?term GSM3309957 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3309nnn/GSM3309... ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3309nnn/GSM3309... GSE117832 1914.91 single hg38 49841170 49841170 42416468.0 223715.0 0.4489 48264585 3.16 39 0.4899 3950647.0 8.19 41878067 7874013 34004054 70.45 68.22 4.27 18250 70 3099922541 0.53 0.8 8.39 2435871 68.4 23.2 78.33 0.36 0.35 1.2 2:17:43 02-27-11:42:46 5764233.0 0.6458 NA
HEK_PRO-seq HEK w/ osTIR1, ZNF143AID PRO-seq Auxin 1 1 PRO human PAIRED HEK293T very intact RNA true_8 8 SRA /project/shefflab/data/guertin/fastq/SRR8608074_PE1.fastq.gz SRR8608074 SRX5407488 HEK_TIR1_ZNF143AID_Auxin_rep4 GSM3618147 HEK-293T cells cell line: HEK-293T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GSM3618147 NA NA NA 1337.94 paired hg38 51533198 51533198 16626152.0 5380555.0 20.8819 40207164 21.98 37 0.5783 4230222.0 10.52 33104378 18769818 14334559.5 35.65 27.82 2.41 325556 38 3099922541 1.0 7591734.5 7591734.5 2807990 16.0 2.4 14.83 0.39 0.37 1.25 2:50:30 02-27-12:15:32 916082.0 0.9097 /project/shefflab/data/guertin/fastq/SRR8608074_PE2.fastq.gz
HEK_ARF_PRO-seq HEK w/ osTIR1, ZNF143AID, ARF PRO-seq Auxin 1 1 PRO human PAIRED HEK293T very degraded library (post Pol liberation) true_8 8 SRA /project/shefflab/data/guertin/fastq/SRR8608070_PE1.fastq.gz SRR8608070 SRX5407484 HEK_TIR1_ZNF143AID_ARF_Auxin_rep4 GSM3618143 HEK-293T cells cell line: HEK-293T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1302.45 paired hg38 53049272 53049272 21262101.0 8863359.0 33.4156 32625384 38.5 17 1.349 3622152.0 11.1 24911965 15309473 9602492.0 29.43 18.1 2.05 252493 38 3099922541 1.0 5434839.0 5434839.0 3997391 18.5 2.4 17.17 0.42 0.39 1.29 2:23:12 02-27-11:48:45 778059.0 0.9163 /project/shefflab/data/guertin/fastq/SRR8608070_PE2.fastq.gz
H9_PRO-seq_1 H9 PRO-seq DMSO 1 1 PRO human PAIRED H9 low pause index; differential analysis true_8 8 SRA /project/shefflab/data/guertin/fastq/H9_DMSO_rep1_PE1.fastq.gz H9_DMSO_rep1 NA H9_DMSO_rep1 GSM4214080 H9 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2469.73 paired hg38 97729860 97729860 34822522.0 17998987.0 36.8342 60442686 38.15 20 0.8896 5408680.0 8.95 48339851 27585022 20754829.0 34.34 21.24 3.26 674956 38 3099922541 1.0 10983354.0 10983354.0 6258301 26.7 10.1 32.63 0.38 0.36 1.23 3:25:37 02-27-12:51:09 3516802.0 0.8774 /project/shefflab/data/guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz
H9_PRO-seq_2 H9 PRO-seq DMSO 2 1 PRO human PAIRED H9 low pause index; differential analysis true_8 8 SRA /project/shefflab/data/guertin/fastq/H9_DMSO_rep2_PE1.fastq.gz H9_DMSO_rep2 NA H9_DMSO_rep2 GSM4214081 H9 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2754.18 paired hg38 115714026 115714026 45847892.0 28610139.0 49.4497 56658510 51.04 20 1.0321 5827176.0 10.28 43719896 25554169 18165727.0 32.06 15.7 3.11 840435 38 3099922541 1.0 9741100.0 9741100.0 6664276 33.8 12.3 41.45 0.39 0.36 1.29 3:45:40 02-27-13:11:12 3047417.0 0.854 /project/shefflab/data/guertin/fastq/H9_DMSO_rep2_PE2.fastq.gz
H9_PRO-seq_3 H9 PRO-seq DMSO 3 1 PRO human PAIRED H9 low pause index; differential analysis true_8 8 SRA /project/shefflab/data/guertin/fastq/H9_DMSO_rep3_PE1.fastq.gz H9_DMSO_rep3 NA H9_DMSO_rep3 GSM4214082 H9 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2340.86 paired hg38 92628962 92628962 34725419.0 18106301.0 39.0943 54838340 40.8 20 0.9769 5405874.0 9.86 43295089 25127415 18167674.5 33.13 19.61 2.98 711009 38 3099922541 1.0 9740520.5 9740520.5 5843431 28.6 10.5 33.89 0.39 0.36 1.28 3:36:20 02-27-13:02:22 1862033.0 0.8825 /project/shefflab/data/guertin/fastq/H9_DMSO_rep3_PE2.fastq.gz
H9_treated_PRO-seq_1 H9 treated PRO-seq 200 nM romidepsin 1 1 PRO human PAIRED H9 high pause index; differential analysis true_8 8 SRA /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_... H9_200nM_romidepsin_rep1 NA H9_200nM_romidepsin_rep1 GSM4214083 H9 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2710.39 paired hg38 111300168 111300168 43631018.0 25201427.0 45.2855 58239430 47.67 20 1.158 6099206.0 10.47 44081295 26072183 18009111.5 30.92 16.18 3.41 655778 38 3099922541 1.0 9869335.0 9869335.0 7715519 53.0 17.1 75.18 0.4 0.38 1.19 3:37:30 02-27-13:03:34 2891628.0 0.8095 /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_...
H9_treated_PRO-seq_2 H9 treated PRO-seq 200 nM romidepsin 2 1 PRO human PAIRED H9 high pause index; differential analysis true_8 8 SRA /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_... H9_200nM_romidepsin_rep2 NA H9_200nM_romidepsin_rep2 GSM4214084 H9 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2737.32 paired hg38 114083518 114083518 43984199.0 27614116.0 48.4104 57348074 49.73 20 1.0037 5458620.0 9.52 44741250 25860518 18880731.5 32.92 16.55 3.37 670904 38 3099922541 1.0 10123508.0 10123508.0 6731776 57.4 16.5 70.88 0.4 0.37 1.16 3:27:15 02-27-12:53:18 2388789.0 0.8186 /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_...
H9_treated_PRO-seq_3 H9 treated PRO-seq 200 nM romidepsin 3 1 PRO human PAIRED H9 high pause index; differential analysis true_8 8 SRA /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_... H9_200nM_romidepsin_rep3 NA H9_200nM_romidepsin_rep3 GSM4214085 H9 cells NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2905.11 paired hg38 120377388 120377388 46004533.0 26667722.0 44.3069 64640918 46.3 20 0.9116 6696846.0 10.36 50176577 29080016 21096561.0 32.64 17.53 3.98 667197 38 3099922541 1.0 11412874.5 11412874.5 7400125 60.1 17.8 74.17 0.4 0.38 1.1 3:27:30 02-27-12:54:05 4932446.0 0.7916 /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_...

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Looper project objects

Figures
Fig.0 Library complexity file
Fig.1 Gene counts table